rs156666

Variant names:

• chr5-115928156-A-G
• rs156666

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.666 in 152,124 control chromosomes in the GnomAD database, including 35,630 homozygotes. In-silico tool predicts a benign outcome for this variant. 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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101275 AN: 152004 Hom.: 35636 Cov.: 33

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.674

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.666 AC: 101292 AN: 152124 Hom.: 35630 Cov.: 33 AF XY: 0.665 AC XY: 49435 AN XY: 74338

African (AFR) AF: 0.445 AC: 18471 AN: 41486

American (AMR) AF: 0.666 AC: 10178 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2486 AN: 3472

East Asian (EAS) AF: 0.474 AC: 2442 AN: 5152

South Asian (SAS) AF: 0.612 AC: 2949 AN: 4818

European-Finnish (FIN) AF: 0.815 AC: 8624 AN: 10584

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53740 AN: 68002

Other (OTH) AF: 0.672 AC: 1420 AN: 2112

Alfa AF: 0.746 Hom.: 183059

Bravo AF: 0.644

Asia WGS AF: 0.554 AC: 1926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.91
DANN	Benign	0.87
PhyloP100		-0.11

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs156666; hg19: chr5-115263853; COSMIC: COSV60185504;