CYP21A2c.1439G>TLikely benign

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Variant interpretation report

CYP21A2 c.1439G>T, p.(Arg480Leu)

NM_000500.9:c.1439G>T NP_000491.4:p.(Arg480Leu) View identifiers

Classification

Likely benign

Variant description:

No variant summary was recorded for this case.

Five-step scale from benign to pathogenic. This variant is likely benign. Select a step to read what it means.

Likely benign.A likely benign classification under the recorded framework.

In plain language

Gene-level background from the recorded interpretation.

About CYP21A2

No gene-level summary was recorded for this case.

Key facts

Evidence used: 3 supporting (benign) · 1 supporting (pathogenic)
Expert rules: Not recorded
Other laboratories (ClinVar): 3 Benign · 2 Uncertain significance · 1 Likely benign · 1 likely benign · 1 Likely Benign
Pipeline record: 11 Jun 2026

Evidence considered

View criteria

Applied evidence criteria

PS3 (supporting): Functional studies in transiently transfected COS-1 cells demonstrated that the p.Arg480Leu (R479L in older numbering) mutant retains approximately 75-80% of wild-type 21-hydroxylase activity toward both 17-hydroxyprogesterone and progesterone, consistent with a mild non-classical CAH phenotype. This partial reduction in enzyme activity supports a damaging effect at the supporting level.
BS1 (supporting): BS1 requires allele frequency >0.3% in population databases for a recessive disorder. The variant is present in gnomAD v2.1 at global AF 0.62% (1521/244182 alleles) and in v4.1 at global AF 0.33% (5128/1571116 alleles). Both exceed the 0.3% threshold. Additionally, the variant was observed in heterozygous state in 1 of 92 healthy individuals in a Hungarian population study (PMID:19505723).
BP4 (supporting): BP4 requires multiple lines of computational evidence suggesting no impact. REVEL score is 0.334 (below 0.5 pathogenic threshold), BayesDel score is -0.316 (negative, predicts benign), and SpliceAI predicts no splice impact (max delta 0.00). All three in silico tools consistently predict a benign effect.
BP6 (supporting): BP6 applies when a reputable source reports the variant as benign without access to the underlying evidence. ClinVar reports this variant as Benign by 3 clinical laboratories, Likely benign by 3 additional laboratories, and VUS by 2 laboratories. The majority clinical consensus across multiple submitters supports a benign interpretation.

LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.

01The reasoning

How it was classified

The recorded framework is Not recorded. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.

Recorded applied criteria

The applied criteria and their strengths are shown as assessed under the stated framework.

Pathogenic evidence criteria: 1 Benign evidence criteria: 3

Pathogenic criteria applied · 1

PS3Supporting

PS3 · supporting

Functional studies in transiently transfected COS-1 cells demonstrated that the p.Arg480Leu (R479L in older numbering) mutant retains approximately 75-80% of wild-type 21-hydroxylase activity toward both 17-hydroxyprogesterone and progesterone, consistent with a mild non-classical CAH phenotype. This partial reduction in enzyme activity supports a damaging effect at the supporting level.

Benign criteria applied · 3

BS1Supporting

BS1 · supporting

BS1 requires allele frequency >0.3% in population databases for a recessive disorder. The variant is present in gnomAD v2.1 at global AF 0.62% (1521/244182 alleles) and in v4.1 at global AF 0.33% (5128/1571116 alleles). Both exceed the 0.3% threshold. Additionally, the variant was observed in heterozygous state in 1 of 92 healthy individuals in a Hungarian population study (PMID:19505723).

BP4Supporting

BP4 · supporting

BP4 requires multiple lines of computational evidence suggesting no impact. REVEL score is 0.334 (below 0.5 pathogenic threshold), BayesDel score is -0.316 (negative, predicts benign), and SpliceAI predicts no splice impact (max delta 0.00). All three in silico tools consistently predict a benign effect.

BP6Supporting

BP6 · supporting

BP6 applies when a reputable source reports the variant as benign without access to the underlying evidence. ClinVar reports this variant as Benign by 3 clinical laboratories, Likely benign by 3 additional laboratories, and VUS by 2 laboratories. The majority clinical consensus across multiple submitters supports a benign interpretation.

Recorded classification: Likely benign

gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PS3 supporting, BS1 supporting benign, BP4 supporting benign, BP6 supporting benign; combination = 1 supporting + 3 supporting benign, which maps to Likely Benign.

02The sources

Evidence at a glance

Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.

gnomAD v4.1

gnomAD v2.1

Population frequency

5,128 / 1,571,116 alleles

gnomAD v4.1: 5,128 / 1,571,116 alleles. Recorded AF 0.00326392. Recorded homozygote count 1.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 0.00622896; MAF= 0.62290%, 1521/244182 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.0607908; MAF= 6.07908%, 1316/21648 alleles, homozygotes = 0); grpmax FAF= 0.0615449.

Applied · BS1 →

gnomAD v4.1 ↗gnomAD v2.1 ↗gnomAD-Canada ↗

SpliceAI score

0.000 maximum delta

Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.

Applied · BP4 → SpliceAI ↗

ClinVar submissions

8 reported laboratory submissions

3 Benign · 2 Uncertain significance · 1 Likely benign · 1 likely benign · 1 Likely Benign.

Applied · BP6 → ClinVar ↗

No screenshot for this evidence

Functional evidence

Not recorded

No standalone functional evidence summary is recorded in evidence_summary.functional.

Applied · PS3 → OncoKB ↗

COSMIC

Cancer Hotspots

Somatic evidence

3 recorded samples

This variant has previously been reported in somatic cancers (COSMIC; COSV99056687, n = 3 times).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.

Context only

COSMIC ↗Cancer Hotspots ↗

For specialists

Technical detail

ACMG/AMP criteria under Not recorded, with the data and sources behind each one.

26 criteria with recorded statuses: 4 met · 13 not met · 5 not assessed · 4 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.

Pathogenic

PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM5 PM6 PP1 PP2 PP3 PP4 PP5 PS5

Benign

BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP4 BP5 BP6 BP7

Met Not met Not assessed Not applicable

NM_000500.9:c.1439G>T (p.Arg480Leu) is a missense variant in exon 10 of CYP21A2, a gene associated with autosomal recessive congenital adrenal hyperplasia due to 21-hydroxylase deficiency.

The variant is present in gnomAD at an appreciable global allele frequency of 0.62% (v2.1, 1521/244182 alleles) and 0.33% (v4.1, 5128/1571116 alleles), exceeding the BS1 threshold (>0.3%) for a recessive disorder.

In silico predictions are uniformly benign: REVEL score 0.334, BayesDel score -0.316 (predicting benign), and SpliceAI detects no splice alteration (max delta 0.00), satisfying BP4.

ClinVar reports this variant as Benign by three clinical laboratories and Likely benign by three additional laboratories, with two VUS submissions, supporting BP6.

Functional studies demonstrate the variant retains ~75-80% of wild-type 21-hydroxylase activity in transfected COS-1 cells, consistent with a mild functional impact, providing PS3 at the supporting level.

Applying the generic ACMG/AMP 2015 combination rules (PMID:25741868), the criteria met are three supporting benign (BS1, BP4, BP6) and one supporting pathogenic (PS3). Likely benign requires at least two supporting benign criteria, which is satisfied.

Met · 4

PS3 SupportingFunctional studies in transiently transfected COS-1 cells demonstrated that the p.Arg480Leu (R479L in older numbering) mutant retains approximately 75-80% of wild-type 21-hydroxylase activity toward both 17-hydroxyprogesterone and progesterone, consistent with a mild non-classical CAH phenotype. This partial reduction in enzyme activity supports a damaging effect at the supporting level. Details ▾Hide ▴

Evidence considered

PMID:17119906 (Robins et al. 2007): R479L showed 75.5% (SD 15.7%) activity for 17OHP and 79.6% (SD 12%) for progesterone vs WT in COS-1 cells
kinetic analysis showed normal Km but mildly reduced Vmax

Still missing

Additional independent functional replication would strengthen the evidence
the residual activity is only mildly reduced
limiting strength to supporting

Sources

PMID:17119906 ↗17119906

BS1 SupportingBS1 requires allele frequency >0.3% in population databases for a recessive disorder. The variant is present in gnomAD v2.1 at global AF 0.62% (1521/244182 alleles) and in v4.1 at global AF 0.33% (5128/1571116 alleles). Both exceed the 0.3% threshold. Additionally, the variant was observed in heterozygous state in 1 of 92 healthy individuals in a Hungarian population study (PMID:19505723). Details ▾Hide ▴

Evidence considered

gnomAD v2.1 global AF: 0.62%
gnomAD v4.1 global AF: 0.33%
PMID:19505723: R479L found in 1/92 healthy Hungarian individuals

Sources

gnomad_v2 ↗gnomad_v4 ↗PMID:19505723 ↗19505723

BP4 SupportingBP4 requires multiple lines of computational evidence suggesting no impact. REVEL score is 0.334 (below 0.5 pathogenic threshold), BayesDel score is -0.316 (negative, predicts benign), and SpliceAI predicts no splice impact (max delta 0.00). All three in silico tools consistently predict a benign effect. Details ▾Hide ▴

Evidence considered

REVEL: 0.334 (benign range)
BayesDel: -0.315808 (predicts benign)
SpliceAI: max delta 0.00 (no splice impact)

Sources

revelbayesdelspliceai ↗

BP6 SupportingBP6 applies when a reputable source reports the variant as benign without access to the underlying evidence. ClinVar reports this variant as Benign by 3 clinical laboratories, Likely benign by 3 additional laboratories, and VUS by 2 laboratories. The majority clinical consensus across multiple submitters supports a benign interpretation. Details ▾Hide ▴

Evidence considered

ClinVar (VariationID 445854): Benign (3 labs)
Likely benign (3 labs)
VUS (2 labs)
review status: criteria provided
single submitter

Still missing

ClinVar review status is single-submitter level
no expert panel review

Sources

clinvar ↗

Not met · 13 · evaluated, threshold not reached

PS2 No confirmed de novo occurrence with both parents confirmed unaffected was identified for this variant. PS2 requires a de novo variant with maternity and paternity confirmed. Details ▾Hide ▴

Evidence considered

No confirmed de novo report identified

Still missing

No de novo family study data available

PS4 PS4 requires the prevalence of the variant in affected individuals to be significantly increased compared to controls. No formal case-control study is available. The variant is present at appreciable frequency in the general population (gnomAD global AF 0.33-0.62%), which precludes PS4 applicability. Details ▾Hide ▴

Evidence considered

gnomAD v2.1: global AF 0.62% (1521/244182 alleles)
gnomAD v4.1: global AF 0.33% (5128/1571116 alleles)
No case-control comparison available

Still missing

No formal case-control study comparing variant frequency in CAH patients vs controls

Sources

gnomad_v2 ↗gnomad_v4 ↗

PM1 PM1 requires location in a mutational hot spot or critical functional domain without benign variation. While Arg480 lies in the C-terminal region (exon 10) near the heme-binding domain, the variant is present in gnomAD at appreciable frequency (AF 0.33-0.62% globally, up to 6% in African population, with 1 homozygote in v4.1), indicating that benign variation exists at this position. Cancer Hotspots analysis confirms the residue is not in a statistically significant hotspot. Details ▾Hide ▴

Evidence considered

Cancer Hotspots: residue not significant
exact variant not listed as hotspot
gnomAD: appreciable population frequency with 1 homozygote in v4.1
inconsistent with a domain devoid of benign variation

Still missing

No VCEP-defined critical domain boundaries for CYP21A2

Sources

gnomad_v2 ↗gnomad_v4 ↗

PM2 PM2 requires the variant to be absent or at extremely low frequency in population databases (<0.1%). The variant is present in gnomAD v2.1 at global AF 0.62% and in v4.1 at global AF 0.33%, both well above the 0.1% threshold. Details ▾Hide ▴

Evidence considered

gnomAD v2.1: AF 0.62% (1521/244182 alleles
0 homozygotes)
gnomAD v4.1: AF 0.33% (5128/1571116 alleles
1 homozygote)

Sources

gnomad_v2 ↗gnomad_v4 ↗

PM6 PM6 requires an assumed de novo occurrence without confirmation of both parents. No verified de novo report with at least one parent tested negative was confirmed for this variant. Details ▾Hide ▴

Evidence considered

No verified de novo evidence identified

Still missing

No parental testing data available to assess de novo status

PP1 PP1 requires cosegregation with disease in multiple affected family members. No verified segregation data across multiple families was identified for this variant. Details ▾Hide ▴

Evidence considered

No confirmed cosegregation data in multiple families

Still missing

No family segregation studies verified

PP2 PP2 requires a missense variant in a gene with a low rate of benign missense variation where missense variants are a common disease mechanism. CYP21A2 has multiple known benign missense variants (e.g., R102K, N493S), and the variant itself is observed at appreciable population frequency, inconsistent with a low rate of benign missense variation. Details ▾Hide ▴

Evidence considered

CYP21A2 has known benign/common missense polymorphisms (R102K
N493S
+L9 ins)
This variant itself is present at AF 0.33-0.62% in gnomAD

Sources

gnomad_v2 ↗gnomad_v4 ↗

PP3 PP3 requires multiple lines of computational evidence supporting a deleterious effect. All in silico predictors suggest a benign effect: REVEL score 0.334 (below 0.5 pathogenic threshold), BayesDel score -0.316 (negative, predicts benign), and SpliceAI max delta 0.0 (no predicted splice impact). Details ▾Hide ▴

Evidence considered

REVEL: 0.334
BayesDel: -0.315808
SpliceAI: max delta 0.00

Sources

revelbayesdelspliceai ↗

PP5 PP5 requires a reputable source to have recently reported the variant as pathogenic. ClinVar reports this variant predominantly as Benign (3 laboratories) and Likely benign (3 laboratories), with 2 VUS submissions. No reputable source reports it as pathogenic. Details ▾Hide ▴

Evidence considered

ClinVar: Benign (3 labs)
Likely benign (3 labs)
VUS (2 labs)

Sources

clinvar ↗

BA1 BA1 requires allele frequency >1% in population databases. The global allele frequency in gnomAD v2.1 is 0.62% and in v4.1 is 0.33%, both below the 1% threshold. Note: the highest subpopulation frequency (African/African American) is 6.08% (v2.1) and 5.87% (v4.1), which would satisfy BA1; however, using global AF as the primary metric, BA1 is not met. Details ▾Hide ▴

Evidence considered

gnomAD v2.1 global AF: 0.62% (<1%)
gnomAD v4.1 global AF: 0.33% (<1%)
Highest subpopulation AF (African): 6.08% (v2.1)
5.87% (v4.1)

Still missing

Subpopulation AF in African ancestry exceeds BA1 threshold
adjudication may depend on whether global or subpopulation AF is used

Sources

gnomad_v2 ↗gnomad_v4 ↗

BS3 BS3 requires well-established functional studies showing no damaging effect. Functional studies demonstrate that p.Arg480Leu reduces 21-hydroxylase activity to approximately 75-80% of wild-type (PMID:17119906), which is a damaging effect. BS3 does not apply because functional evidence supports pathogenicity, not benignity. Details ▾Hide ▴

Evidence considered

PMID:17119906: residual activity 75-80% of WT
consistent with mild functional impairment

Sources

PMID:17119906 ↗17119906

BS4 BS4 requires lack of segregation in affected family members. No evidence of non-segregation was identified. Details ▾Hide ▴

Evidence considered

No segregation data available for BS4 assessment

Still missing

No family segregation data

BP1 BP1 applies when a missense variant occurs in a gene where primarily truncating variants cause disease. CYP21A2-related congenital adrenal hyperplasia is caused by both missense and truncating variants; missense variants are a well-established disease mechanism. BP1 is not applicable. Details ▾Hide ▴

Evidence considered

CYP21A2 disease mechanism includes both missense and truncating variants
many pathogenic missense variants are known

Not assessed · 5 · no assessment recorded

PS1 PS1 requires a different amino acid change at the same residue that has been previously established as pathogenic. No same-residue pathogenic comparator variant with a different amino acid change was identified in ClinVar or the literature for Arg480. Details ▾Hide ▴

Evidence considered

No same-residue pathogenic comparator variant identified

Still missing

No alternate pathogenic missense at Arg480 identified

PP4 PP4 requires the patient's phenotype or family history to be highly specific for a disease with a single genetic etiology. No individual patient phenotype data was available for assessment. Details ▾Hide ▴

Evidence considered

No patient-specific phenotype data available

Still missing

No individual patient phenotype information

BS2 BS2 requires observation in a healthy adult in a state (homozygous for recessive) where full penetrance is expected at an early age. One homozygote is present in gnomAD v4.1, but the clinical status of this individual is unknown, precluding definitive assessment. Details ▾Hide ▴

Evidence considered

gnomAD v4.1: 1 homozygote of unknown clinical status

Still missing

Clinical status of the homozygous individual in gnomAD v4.1 is unknown

Sources

gnomad_v4 ↗

BP5 BP5 requires the variant to be found in a case with an alternate molecular basis for disease. No such evidence was identified. Details ▾Hide ▴

Evidence considered

No alternate molecular basis evidence identified

Still missing

No patient-level data with alternate molecular diagnoses

PS5 No different pathogenic variant at the same residue reported from a reputable source was identified. Details ▾Hide ▴

Evidence considered

No same-residue pathogenic variant from reputable source

Still missing

No alternate pathogenic variant at Arg480 identified

Not applicable · 4· recorded as not applicable Show reasons ▾Hide reasons ▴

PVS1 N/ANM_000500.9:c.1439G>T is a missense variant (p.Arg480Leu), not a null variant (nonsense, frameshift, canonical ±1/2 splice site, or initiation codon). Generic PVS1 framework (PMC6185798) does not apply to missense variants. Details ▾Hide ▴

Evidence considered

Variant is missense (p.Arg480Leu)
apply_generic_pvs1_framework=false per pvs1_variant_assessment

Sources

pvs1_generic_framework ↗pvs1_variant_assessment

PM5 N/ANo same-residue comparator variant with a different pathogenic missense change was identified; automated PM5 candidate harvesting was unable to confirm classic same-residue PM5 semantics. Details ▾Hide ▴

Evidence considered

PM5 candidate search returned no eligible same-residue candidates

Sources

pm5_candidates

BP2 N/ACYP21A2 is an autosomal recessive gene. BP2 applies to observations in trans with a pathogenic variant in dominant disorders, or in cis with a pathogenic variant in any inheritance pattern. For recessive disorders, observation in trans with a pathogenic variant is expected and does not support benignity. Details ▾Hide ▴

Evidence considered

Recessive disorder
BP2 is not applicable

BP7 N/ABP7 applies to synonymous variants with no predicted splice impact. NM_000500.9:c.1439G>T is a missense variant (p.Arg480Leu), not a synonymous variant. Details ▾Hide ▴

Evidence considered

Variant is missense
not synonymous

Identifiers

Gene: CYP21A2
Transcript: NM_000500.9
Coding (HGVS c.): NM_000500.9:c.1439G>T
Protein (HGVS p.): NP_000491.4:p.(Arg480Leu)
GRCh38: chr6:32041085 G>T
GRCh37: chr6:32008862 G>T
ClinVar: 445854
COSMIC: COSV99056687

Gene diagram

Every interpreted variant in CYP21A2, mapped onto the exon structure of NM_000500.9. Select a row to find it on the plot.

CYP21A2NM_000500.9

Fetching transcript structure from UCSC…

Exons

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Transcript span

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Strand

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Variants mapped

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Source

UCSC ncbiRefSeqCurated

All variants in CYP21A2 — Select a row to find it on the plot; use the link to open its page.

	Protein	Location	Classification	Link

gnomAD v4.1 5,128 / 1,571,116 alleles AF 0.00326 · 1 homozygotes · FAF 0.0572

gnomAD v2.1 1,521 / 244,182 alleles AF 0.00623 · 0 homozygotes · FAF 0.0615

gnomAD-Canada v1.0 0 / 0 alleles AF 0 · 0 homozygotes · FAF 0

By genetic ancestry

gnomAD v4.1

AF 0.0033 · 5128 / 1,571,116 alleles · 1 hom · FAF 0.057

African/African American4316 / 73,584	0.0591 hom
Middle Eastern25 / 4,656	0.0054
Admixed American308 / 58,074	0.0053
Remaining individuals305 / 61,106	0.005
South Asian50 / 88,918	0.00056
European (non-Finnish)124 / 1,159,074	0.00011

0 alternate alleles recorded in 4 other groups: European (Finnish), Amish, East Asian, Ashkenazi Jewish.

gnomAD v2.1

AF 0.0062 · 1521 / 244,182 alleles · 0 hom · FAF 0.062

African/African American1316 / 21,648	0.061
Admixed American140 / 33,094	0.0042
Remaining individuals17 / 6,458	0.0026
South Asian20 / 28,606	0.0007
European (non-Finnish)28 / 111,522	0.00025

0 alternate alleles recorded in 3 other groups: Ashkenazi Jewish, East Asian, European (Finnish).

gnomAD-Canada

AF 0 · 0 / 0 alleles · 0 hom

Statements

gnomAD v4.1

This variant is present in gnomAD v4.1 (AF= 0.00326392; MAF= 0.32639%, 5128/1571116 alleles, homozygotes = 1) and has highest observed frequency in the African/African American population (AF= 0.0586541; MAF= 5.86541%, 4316/73584 alleles, homozygotes = 1); grpmax FAF= 0.0571923.

gnomAD v2.1

Open the gnomAD-Canada detail page →

SpliceAI and Pangolin

Pangolin splice lossmagnitude shown

-0.250

Pangolin splice gain

0.070

Other predictors

REVEL: 0.334
BayesDel: -0.316

How the predictions were used

Evidence considered

REVEL: 0.334 (benign range)
BayesDel: -0.315808 (predicts benign)
SpliceAI: max delta 0.00 (no splice impact)

Sources

revelbayesdelspliceai ↗

Evidence considered

REVEL: 0.334
BayesDel: -0.315808
SpliceAI: max delta 0.00

Sources

revelbayesdelspliceai ↗

BP7 N/ABP7 applies to synonymous variants with no predicted splice impact. NM_000500.9:c.1439G>T is a missense variant (p.Arg480Leu), not a synonymous variant. Details ▾Hide ▴

Evidence considered

Variant is missense
not synonymous

Statement

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.334. BayesDel score = -0.315808.

8 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.

Recorded publications

Detection and assignment of CYP21 mutations using peptide mass signature genotyping.

Zeng X et al. · 2004

No paper-specific finding is recorded.

PMID 15110320 ↗
Molecular model of human CYP21 based on mammalian CYP2C5: structural features correlate with clinical severity of mutations causing congenital adrenal hyperplasia.

Robins T et al. · 2006

No paper-specific finding is recorded.

PMID 16788163 ↗
Characterization of novel missense mutations in CYP21 causing congenital adrenal hyperplasia.

Robins T et al. · 2007

No paper-specific finding is recorded.

PMID 17119906 ↗
Linkage analysis of the C4A/C4B copy number variation and polymorphisms of the adjacent steroid 21-hydroxylase gene in a healthy population.

Blaskó B et al. · 2009

No paper-specific finding is recorded.

PMID 19505723 ↗
A large view of CYP21 locus among Sicilians and other populations: identification of a novel CYP21A2 variant in Sicily.

Niceta M et al. · 2011

No paper-specific finding is recorded.

PMID 21169732 ↗
Carrier testing for severe childhood recessive diseases by next-generation sequencing.

Bell CJ et al. · 2011

No paper-specific finding is recorded.

PMID 21228398 ↗
Intraspecific evolution of human RCCX copy number variation traced by haplotypes of the CYP21A2 gene.

Bánlaki Z et al. · 2013

No paper-specific finding is recorded.

PMID 23241443 ↗
Structure-phenotype correlations of human CYP21A2 mutations in congenital adrenal hyperplasia.

Haider S et al. · 2013

No paper-specific finding is recorded.

PMID 23359706 ↗

Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.

gnomAD v4.1 5,128 / 1,571,116 recorded alleles Open source ↗

gnomAD v2.1 Captured gnomAD v2.1 source record Open source ↗

SpliceAI Lookup Recorded maximum delta 0.000 Open source ↗

ClinVar 3 Benign · 2 Uncertain significance · 1 Likely benign · 1 likely benign · 1 Likely Benign Open source ↗

COSMIC Captured COSMIC source record Open source ↗

Cancer hotspots Captured Cancer Hotspots source record Open source ↗

All source links

Statements for reports

The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.

gnomAD v4.1

gnomAD v2.1

ClinVar

This variant has been reported in ClinVar as Benign (3 clinical laboratories) and as Uncertain significance (2 clinical laboratories) and as Likely benign (1 clinical laboratory) and as likely benign (1 clinical laboratory) and as Likely Benign (1 clinical laboratory). (ClinVarID = 445854)

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.334. BayesDel score = -0.315808.

Somatic

This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV99056687, n = 3 times).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.