rs4942925

Variant names:

• chr13-32807106-T-C
• rs4942925

GermlineCancer (beta)

Variant summary

Our verdict is Benign.

<-10 Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received -12 classification points (ACMG Germline Pathogenicity v2019). BA1BP4_Strong

The variant 13-32807106-T-C has been identified. The variant allele was found at a cumulative frequency of 0.363 (AC=55,234) in the gnomAD database across 152,106 control chromosomes, including 10,742 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.436. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.36 (10742 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 17 publications found

Classification according to ACMG Germline Pathogenicity v2019

Our verdict: Benign. The variant received -12 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	BP4Computational evidence suggests no impact		Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).
	BA1Stand-alone benign allele frequency (>5%)		GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.4363 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

 

RefSeq Transcripts

There are no transcript annotations for this variant.

Ensembl Transcripts

There are no transcript annotations for this variant.

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 4 sources Large-scale international reference populations
GnomAD3 genomes	AF: 0.363	AC:55223	Hom:10745	AN:151988	Cov:32
GnomAD4 genome	AF: 0.363	AC:55234	Hom:10742	AN:152106	Cov:32
TOPMed (Bravo)	AF: 0.357	AC:	Hom:	AN:	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.407	AC:114493	Hom:23869	AN:281642	Cov:
Local & regional cohorts 9 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.391	AC:915	Hom:181	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.167	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.440	AC:132	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.176	AC:618	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.148	AC:1072	Hom:	AN:7234	Cov:
Qatari Genome	AF: 0.290	AC:51	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.158	AC:19454	Hom:1584	AN:122804	Cov:
Turkish Variome	AF: 0.340	AC:525	Hom:100	AN:1546	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.163	AC:1457	Hom:123	AN:8960	Cov:

Showing 13 sources

Tested, but no data found:GnomAD4 exomeIf GnomAD4 is missing, the position is probably not covered by the project.

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	0.83
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
DANN	Benign	0.74
GPN-Star LLR	N/A	0.022
GPN-Star score	N/A	-0.022
PhyloP100	Benign	-0.16

Showing 7 of 7 scores

Splicing Scores

No splicing scores have been computed for this variant.

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

dbSNP: rs4942925;

hg19: chr13-33381244;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar