chr6-15664978-A-T

Variant names:

• chr6-15664978-A-T
• rs2619538

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 6-15664978-A-T has been identified. The variant allele was found at a cumulative frequency of 0.529 (AC=80,488) in the gnomAD database across 152,106 control chromosomes, including 22,520 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.632. 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 0.53 (22520 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.977
• Publications: 43 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 = 0.632 — 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: 0.529	AC:80439	Hom:22515	AN:151988	Cov:32
GnomAD4 genome	AF: 0.529	AC:80488	Hom:22520	AN:152106	Cov:32
TOPMed (Bravo)	AF: 0.542	AC:	Hom:	AN:	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.545	AC:13539	Hom:3745	AN:24820	Cov:
Local & regional cohorts 10 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.573	AC:1342	Hom:392	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.0274	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.503	AC:151	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.188	AC:655	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.0250	AC:178	Hom:	AN:7234	Cov:
Qatari Genome	AF: 0.506	AC:89	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.0273	AC:3351	Hom:60	AN:122642	Cov:
Turkish Variome	AF: 0.457	AC:707	Hom:165	AN:1546	Cov:
UK10K	AF: 0.561	AC:4243	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.0234	AC:210	Hom:5	AN:8960	Cov:

Showing 14 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	0.18
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.20
DANN	Benign	0.56
GPN-Star LLR	N/A	4.3
GPN-Star score	N/A	-0.63
PhyloP100	Benign	-0.98

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: rs2619538;

hg19: chr6-15665209;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar