3-35610457-C-A

Variant names:

• chr3-35610457-C-A
• rs9881157

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 0.735 in 151,956 control chromosomes in the GnomAD database, including 41,345 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 0.74 (41345 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.827 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: 0.735 AC: 111637 AN: 151838 Hom.: 41309 Cov.: 31

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.735 AC: 111723 AN: 151956 Hom.: 41345 Cov.: 31 AF XY: 0.731 AC XY: 54307 AN XY: 74270

African (AFR) AF: 0.834 AC: 34580 AN: 41466

American (AMR) AF: 0.689 AC: 10513 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2343 AN: 3470

East Asian (EAS) AF: 0.649 AC: 3340 AN: 5144

South Asian (SAS) AF: 0.793 AC: 3819 AN: 4818

European-Finnish (FIN) AF: 0.638 AC: 6727 AN: 10552

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.708 AC: 48098 AN: 67938

Other (OTH) AF: 0.715 AC: 1512 AN: 2114

Alfa AF: 0.717 Hom.: 48407

Bravo AF: 0.739

Asia WGS AF: 0.710 AC: 2468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.18
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9881157; hg19: chr3-35651949;