8-11486464-C-T

Variant names:

• chr8-11486464-C-T
• rs2736340

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 8-11486464-C-T has been identified. The variant allele was found at a cumulative frequency of 0.259 (AC=39,418) in the gnomAD database across 152,104 control chromosomes, including 6,491 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.696. 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 0.26 (6491 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.878
• Publications: 210 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 = 0.696 — 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: 0.259	AC:39383	Hom:6471	AN:151986	Cov:32
GnomAD4 genome	AF: 0.259	AC:39418	Hom:6491	AN:152104	Cov:32
TOPMed (Bravo)	AF: 0.274	AC:	Hom:	AN:	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.263	AC:186917	Hom:28163	AN:710204	Cov:
Local & regional cohorts 10 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.266	AC:624	Hom:80	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.731	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.263	AC:79	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.534	AC:1855	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.727	AC:5253	Hom:	AN:7230	Cov:
Qatari Genome	AF: 0.256	AC:45	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.693	AC:85027	Hom:29474	AN:122752	Cov:
Turkish Variome	AF: 0.272	AC:421	Hom:55	AN:1546	Cov:
UK10K	AF: 0.259	AC:1956	Hom:	AN:7562	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.731	AC:6550	Hom:2367	AN:8960	Cov:

Showing 14 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	1.4
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.72
GPN-Star LLR	N/A	-1.4
GPN-Star score	N/A	1.4
PhyloP100	Benign	0.88
PromoterAI	N/A	-0.0080	Neutral

Showing 8 of 8 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: rs2736340;

hg19: chr8-11343973;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar