rs10476156

Variant names:

• chr5-175435667-A-G
• rs10476156

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 0.155 in 151,552 control chromosomes in the GnomAD database, including 1,886 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 0.15 (1886 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.591
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23408 AN: 151432 Hom.: 1885 Cov.: 28

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.155 AC: 23423 AN: 151552 Hom.: 1886 Cov.: 28 AF XY: 0.155 AC XY: 11459 AN XY: 74012

African (AFR) AF: 0.170 AC: 7022 AN: 41344

American (AMR) AF: 0.192 AC: 2926 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 404 AN: 3458

East Asian (EAS) AF: 0.191 AC: 966 AN: 5058

South Asian (SAS) AF: 0.107 AC: 511 AN: 4772

European-Finnish (FIN) AF: 0.127 AC: 1343 AN: 10550

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.145 AC: 9808 AN: 67856

Other (OTH) AF: 0.156 AC: 325 AN: 2084

Alfa AF: 0.155 Hom.: 281

Bravo AF: 0.165

Asia WGS AF: 0.141 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.29
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs10476156; hg19: chr5-174862670; COSMIC: COSV107510578;