3-39541433-C-T

Variant names:

• chr3-39541433-C-T
• rs1606473

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 3-39541433-C-T has been identified. The variant allele was found at a cumulative frequency of 0.613 (AC=93,112) in the gnomAD database across 151,952 control chromosomes, including 32,365 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.765. 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 0.61 (32365 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.881
• Publications: 3 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 = 0.7646 — 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: 0.613	AC:93117	Hom:32369	AN:151836	Cov:31
GnomAD4 genome	AF: 0.613	AC:93112	Hom:32365	AN:151952	Cov:31
TOPMed (Bravo)	AF: 0.588	AC:	Hom:	AN:	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.714	AC:75922	Hom:28478	AN:106274	Cov:
Local & regional cohorts 10 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.638	AC:1494	Hom:503	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.638	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.780	AC:234	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.611	AC:2126	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.656	AC:4748	Hom:	AN:7234	Cov:
Qatari Genome	AF: 0.591	AC:104	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.615	AC:75389	Hom:23238	AN:122604	Cov:
Turkish Variome	AF: 0.761	AC:1177	Hom:447	AN:1546	Cov:
UK10K	AF: 0.782	AC:5913	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.630	AC:5643	Hom:1771	AN:8960	Cov:

Showing 14 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	1.2
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.44
DANN	Benign	0.58
GPN-Star LLR	N/A	-0.56
GPN-Star score	N/A	0.56
PhyloP100	Benign	-0.88

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: rs1606473;

hg19: chr3-39582924;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar