rs156666

Variant names:

• chr5-115928156-A-G
• rs156666

GermlineCancer (beta)

Variant summary

Our verdict is Benign.

<-10 Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received -12 classification points (ACMG Germline Pathogenicity v2019). BA1BP4_Strong

The variant 5-115928156-A-G has been identified. The variant allele was found at a cumulative frequency of 0.666 (AC=101,292) in the gnomAD database across 152,124 control chromosomes, including 35,630 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.785. 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 0.67 (35630 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 2 publications found

Classification according to ACMG Germline Pathogenicity v2019

Our verdict: Benign. The variant received -12 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	BP4Computational evidence suggests no impact		Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).
	BA1Stand-alone benign allele frequency (>5%)		GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.7847 — exceeds 5%% threshold (BA1 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: 0.666	AC:101275	Hom:35636	AN:152004	Cov:33
GnomAD4 genome	AF: 0.666	AC:101292	Hom:35630	AN:152124	Cov:33
TOPMed (Bravo)	AF: 0.644	AC:170427	Hom:57948	AN:264690	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.744	AC:494087	Hom:187656	AN:664076	Cov:
Local & regional cohorts 9 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.669	AC:1566	Hom:539	AN:2342	Cov:
ChinaMAP Phase 1	AF: 0.444	AC:	Hom:	AN:	Cov:
Denmark Genome	AF: 0.720	AC:216	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.554	AC:1926	Hom:	AN:3478	Cov:
Korea4K (4,157 Koreans)	AF: 0.448	AC:3240	Hom:	AN:7234	Cov:
Qatari Genome	AF: 0.580	AC:102	Hom:	AN:176	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.444	AC:54521	Hom:12151	AN:122806	Cov:
Turkish Variome	AF: 0.690	AC:1065	Hom:365	AN:1544	Cov:
WBBC (Westlake BioBank for Chinese) pilot	AF: 0.472	AC:4232	Hom:1006	AN:8960	Cov:

Showing 13 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	0.72
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.91
DANN	Benign	0.87
GPN-Star LLR	N/A	-0.0050
GPN-Star score	N/A	0.0050
PhyloP100	Benign	-0.11

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: rs156666;

hg19: chr5-115263853;

COSMIC: COSV60185504;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar