About CCND1
No gene-level summary was recorded for this case.
No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is benign. Select a step to read what it means.
Benign.A benign classification under the recorded framework.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.No gene-level summary was recorded for this case.
The recorded framework is Not recorded. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
The applied criteria and their strengths are shown as assessed under the stated framework.
No pathogenic criterion marked as applied in the recorded assessment.
Allele frequency far exceeds the 1% BA1 threshold: 44.66% in gnomAD v2.1 (125,943/282,012 alleles, 29,329 homozygotes) and 44.40% in gnomAD v4.1 (716,284/1,613,168 alleles, 162,210 homozygotes). This is a common polymorphism present in all populations, with highest frequency in East Asians (56.69% in v2.1).
Allele frequency exceeds the 0.3% BS1 threshold. Superseded by BA1 for classification purposes but independently meets BS1 criteria.
Observed in 29,329 homozygous individuals in gnomAD v2.1 and 162,210 homozygous individuals in gnomAD v4.1. This high number of healthy adult homozygotes demonstrates compatibility with normal development and excludes pathogenicity for any early-onset, fully penetrant Mendelian disorder.
Multiple lines of computational evidence suggest no impact on the gene product. SpliceAI max delta = 0.02 predicts no splicing effect. The variant is synonymous (p.Pro241=) and does not alter the amino acid sequence. REVEL and BayesDel scores are unavailable, as expected for a synonymous variant with no amino acid change.
ClinVar reports this variant as Benign (Variation ID 13755) with review status 'criteria provided, single submitter,' from 2 clinical laboratories. A reputable source classifies this variant as benign.
Synonymous variant (p.Pro241=) at a nucleotide position where SpliceAI predicts no splicing impact (max delta = 0.02). The variant does not alter the amino acid sequence and is not predicted to affect splicing, meeting BP7 criteria.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: BA1 stand-alone benign, BS1 strong benign, BS2 strong benign, BP4 supporting benign, BP6 supporting benign, BP7 supporting benign; combination = 1 stand-alone benign + 2 strong benign + 3 supporting benign, which maps to Benign.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 716,284 / 1,613,168 alleles. Recorded AF 0.444023. Recorded homozygote count 162210.
This variant is present in gnomAD v2.1 (AF= 0.446587; MAF= 44.65874%, 125943/282012 alleles, homozygotes = 29329) and has highest observed frequency in the East Asian population (AF= 0.566911; MAF= 56.69110%, 11294/19922 alleles, homozygotes = 3160); grpmax FAF= 0.559639.
This variant is present in gnomAD-Canada v1.0 (AF= 0.4660823170731707, 8561/18368 alleles, homozygotes = 2065).
Recorded SpliceAI maximum delta score: 0.020. Refer to the recorded PP3/BP4 rationale for interpretation.
2 Benign. ClinVar API review status: criteria provided, multiple submitters, no conflicts.
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
This variant has previously been reported in somatic cancers (COSMIC; COSV57118864, n = 79 times).
This variant does not lie in a statistically significant hotspot.
ACMG/AMP criteria under Not recorded, with the data and sources behind each one.
26 criteria with recorded statuses: 6 met · 7 not met · 8 not assessed · 5 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
NM_053056.3:c.723G>A (p.Pro241=) is a synonymous variant in CCND1 with an allele frequency of 44.66% in gnomAD v2.1 (125,943/282,012 alleles, 29,329 homozygotes) and 44.40% in gnomAD v4.1, meeting BA1 (stand-alone benign).
The variant has been observed in 29,329 homozygous individuals in gnomAD v2.1, demonstrating compatibility with normal health and meeting BS2.
ClinVar classifies this variant as Benign (Variation ID 13755, 2 clinical laboratories), meeting BP6.
SpliceAI predicts no splicing impact (max delta = 0.02) and the variant is synonymous (p.Pro241=), meeting BP7 and BP4.
No publications identified in the case materials mention NM_053056.3:c.723G>A specifically; papers cited by ClinVar submissions discuss the CCND1 c.870G>A polymorphism which is a different variant.
No criteria match.
Every interpreted variant in CCND1, mapped onto the exon structure of NM_053056.3. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
| East Asian23571 / 44,848 | 0.536204 hom |
| South Asian47620 / 91,060 | 0.5212712 hom |
| Middle Eastern3108 / 6,058 | 0.51824 hom |
| European (Finnish)30437 / 63,546 | 0.487327 hom |
| Remaining individuals28397 / 62,486 | 0.456540 hom |
| European (non-Finnish)530242 / 1,179,672 | 0.45119379 hom |
| Ashkenazi Jewish13148 / 29,600 | 0.442908 hom |
| Amish360 / 912 | 0.3968 hom |
| Admixed American23115 / 59,992 | 0.394492 hom |
| African/African American16286 / 74,994 | 0.221756 hom |
| East Asian11294 / 19,922 | 0.573160 hom |
| South Asian15976 / 30,590 | 0.524244 hom |
| European (Finnish)12189 / 25,070 | 0.493030 hom |
| European (non-Finnish)59874 / 128,642 | 0.4713989 hom |
| Remaining individuals3328 / 7,198 | 0.46807 hom |
| Ashkenazi Jewish4635 / 10,328 | 0.451034 hom |
| Admixed American13309 / 35,362 | 0.382483 hom |
| African/African American5338 / 24,900 | 0.21582 hom |
This variant is present in gnomAD v4.1 (AF= 0.444023; MAF= 44.40232%, 716284/1613168 alleles, homozygotes = 162210) and has highest observed frequency in the East Asian population (AF= 0.525575; MAF= 52.55753%, 23571/44848 alleles, homozygotes = 6204); grpmax FAF= 0.519956.
This variant is present in gnomAD v2.1 (AF= 0.446587; MAF= 44.65874%, 125943/282012 alleles, homozygotes = 29329) and has highest observed frequency in the East Asian population (AF= 0.566911; MAF= 56.69110%, 11294/19922 alleles, homozygotes = 3160); grpmax FAF= 0.559639.
This variant is present in gnomAD-Canada v1.0 (AF= 0.4660823170731707, 8561/18368 alleles, homozygotes = 2065).
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02).
7 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.
These translocations cause transcriptional activation of FGFR3/MMSET and CCND1 which contribute to MM biology.
Full text reviewed; paper discusses c.870G>A (rs603965), not c.723G>A.
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
This variant is present in gnomAD v4.1 (AF= 0.444023; MAF= 44.40232%, 716284/1613168 alleles, homozygotes = 162210) and has highest observed frequency in the East Asian population (AF= 0.525575; MAF= 52.55753%, 23571/44848 alleles, homozygotes = 6204); grpmax FAF= 0.519956.
This variant is present in gnomAD v2.1 (AF= 0.446587; MAF= 44.65874%, 125943/282012 alleles, homozygotes = 29329) and has highest observed frequency in the East Asian population (AF= 0.566911; MAF= 56.69110%, 11294/19922 alleles, homozygotes = 3160); grpmax FAF= 0.559639.
This variant is present in gnomAD-Canada v1.0 (AF= 0.4660823170731707, 8561/18368 alleles, homozygotes = 2065).
This variant has been reported in ClinVar as Benign (2 clinical laboratories). (ClinVarID = 13755)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02).
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV57118864, n = 79 times).
This variant does not lie in a statistically significant hotspot.