rs7927894

Variant names:

• chr11-76590272-C-T
• rs7927894

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 11-76590272-C-T has been identified. The variant allele was found at a cumulative frequency of 0.349 (AC=53,046) in the gnomAD database across 151,950 control chromosomes, including 9,453 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.38. 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 0.35 (9453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 110 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 = 0.38 — 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: 0.349	AC:53025	Hom:9453	AN:151832	Cov:32
GnomAD4 genome	AF: 0.349	AC:53046	Hom:9453	AN:151950	Cov:32
TOPMed (Bravo)	AF: 0.351	AC:	Hom:	AN:	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.370	AC:136354	Hom:25842	AN:368028	Cov:
Local & regional cohorts 10 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.339	AC:795	Hom:143	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.181	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.393	AC:118	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.275	AC:956	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.181	AC:1306	Hom:	AN:7232	Cov:
Qatari Genome	AF: 0.415	AC:73	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.137	AC:16775	Hom:1201	AN:122640	Cov:
Turkish Variome	AF: 0.337	AC:521	Hom:94	AN:1544	Cov:
UK10K	AF: 0.398	AC:3010	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.190	AC:1706	Hom:161	AN:8960	Cov:

Showing 14 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	1.0
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.38
GPN-Star LLR	N/A	0.14
GPN-Star score	N/A	-0.14
PhyloP100	Benign	-0.27

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: rs7927894;

hg19: chr11-76301316;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar