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.

• BP4: Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).
• BA1: 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
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	0.666	101275	35636	152004	33
GnomAD4 genome	0.666	101292	35630	152124	33
TOPMed (Bravo)	0.644	170427	57948	264690
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	0.744	494087	187656	664076
Local & regional cohorts 9 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	0.669	1566	539	2342
ChinaMAP Phase 1	0.444
Denmark Genome	0.720	216		300
GenomeAsia100K	0.554	1926		3478
Korea4K (4,157 Koreans)	0.448	3240		7234
Qatari Genome	0.580	102		176
ToMMo 61KJPN (+60KJPN MNV)	0.444	54521	12151	122806
Turkish Variome	0.690	1065	365	1544
WBBC (Westlake BioBank for Chinese) pilot	0.472	4232	1006	8960

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 prediction	Prediction	Score
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

Other links and lift over

dbSNP: rs156666;

hg19: chr5-115263853;

COSMIC: COSV60185504;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar