rs10476156

Positions:

• chr5-175435667-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.156

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10476156; hg19: chr5-174862670;