rs7561317

Variant names:

• chr2-644953-A-G
• rs7561317

Your query was ambiguous. Multiple possible variants found:

• chr2-644953-A-G
• chr2-644953-A-T

GermlineCancer (beta)

Variant summary

Our verdict is Likely benign.

-4 Likely Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received -4 classification points (ACGS-UK Somatic Oncogenicity v2025). B1_Strong

The variant 2-644953-A-G has been identified. The variant allele was found at a cumulative frequency of 0.817 (AC=124,340) in the gnomAD database across 152,184 control chromosomes, including 50,952 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.897. 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 0.82 (50952 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 107 publications found

Classification according to ACGS-UK Somatic Oncogenicity v2025

Our verdict: Likely_benign. The variant received -4 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	B1High frequency in general population		GnomAD effective popmax AF >1% — B1 stand-alone benign; GnomAD effective popmax AF = 0.897 — exceeds 1% threshold (B1 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: 0.817	AC:124264	Hom:50931	AN:152066	Cov:33
GnomAD4 genome	AF: 0.817	AC:124340	Hom:50952	AN:152184	Cov:33
TOPMed (Bravo)	AF: 0.814	AC:215370	Hom:87888	AN:264690	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.822	AC:516041	Hom:212313	AN:628074	Cov:
Local & regional cohorts 10 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.826	AC:1934	Hom:806	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.906	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.740	AC:222	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.883	AC:3071	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.909	AC:6578	Hom:	AN:7234	Cov:
Qatari Genome	AF: 0.795	AC:140	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.905	AC:111193	Hom:50335	AN:122820	Cov:
Turkish Variome	AF: 0.778	AC:1203	Hom:473	AN:1546	Cov:
UK10K	AF: 0.828	AC:6262	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.915	AC:8197	Hom:3750	AN:8960	Cov:

Showing 14 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	4.4
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.8
DANN	Benign	0.69
GPN-Star LLR	N/A	0.60
GPN-Star score	N/A	-0.60
PhyloP100	Benign	0.12

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: rs7561317;

hg19: chr2-644953;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar