rs17762633

Variant names:

• chr3-148665285-A-C
• rs17762633

Your query was ambiguous. Multiple possible variants found:

• chr3-148665285-A-C
• chr3-148665285-A-T

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 0.0835 in 152,100 control chromosomes in the GnomAD database, including 722 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 0.084 (722 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.197 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: 0.0835 AC: 12695 AN: 151982 Hom.: 721 Cov.: 32

Gnomad AFR AF: 0.0210

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0646

Gnomad ASJ AF: 0.0952

Gnomad EAS AF: 0.0697

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.0878

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0835 AC: 12701 AN: 152100 Hom.: 722 Cov.: 32 AF XY: 0.0831 AC XY: 6183 AN XY: 74366

African (AFR) AF: 0.0209 AC: 867 AN: 41494

American (AMR) AF: 0.0645 AC: 984 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0952 AC: 330 AN: 3466

East Asian (EAS) AF: 0.0697 AC: 360 AN: 5168

South Asian (SAS) AF: 0.207 AC: 998 AN: 4812

European-Finnish (FIN) AF: 0.0878 AC: 930 AN: 10594

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7933 AN: 67986

Other (OTH) AF: 0.0814 AC: 172 AN: 2112

Alfa AF: 0.0994 Hom.: 1044

Bravo AF: 0.0759

Asia WGS AF: 0.152 AC: 528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.5
DANN	Benign	0.77
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs17762633; hg19: chr3-148383072;