chr8-116618444-A-C

Variant names:

• chr8-116618444-A-C
• rs16892766

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 8-116618444-A-C has been identified. The variant allele was found at a cumulative frequency of 0.0913 (AC=13,900) in the gnomAD database across 152,184 control chromosomes, including 752 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.124. 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 0.091 (752 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.26
• Publications: 192 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 = 0.124 — 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: 0.0914	AC:13895	Hom:751	AN:152066	Cov:32
GnomAD4 genome	AF: 0.0913	AC:13900	Hom:752	AN:152184	Cov:32
TOPMed (Bravo)	AF: 0.0879	AC:23272	Hom:1237	AN:264690	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.0803	AC:64209	Hom:2804	AN:799766	Cov:
Local & regional cohorts 9 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.0739	AC:173	Hom:7	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.000886	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.111	AC:33	Hom:	AN:296	Cov:
GenomeAsia100K	AF: 0.0460	AC:161	Hom:	AN:3476	Cov:
Qatari Genome	AF: 0.190	AC:33	Hom:	AN:174	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.0000900	AC:11	Hom:1	AN:122252	Cov:
Turkish Variome	AF: 0.0912	AC:141	Hom:10	AN:1546	Cov:
UK10K	AF: 0.0836	AC:632	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.000558	AC:5	Hom:0	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	Uncertain	17
BayesDel_noAF	Benign	-0.39
CADD	Benign	22
DANN	Benign	0.75
GPN-Star LLR	N/A	-4.8
GPN-Star score	N/A	4.8
PhyloP100	Uncertain	4.3

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: rs16892766;

hg19: chr8-117630683;

COSMIC: COSV58902220;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar