rs342758

Variant names:

• chr3-32513688-A-C
• rs342758

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 0.574 in 151,980 control chromosomes in the GnomAD database, including 25,714 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 0.57 (25714 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 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: 0.574 AC: 87189 AN: 151862 Hom.: 25682 Cov.: 32

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.574 AC: 87272 AN: 151980 Hom.: 25714 Cov.: 32 AF XY: 0.565 AC XY: 42004 AN XY: 74288

African (AFR) AF: 0.705 AC: 29237 AN: 41472

American (AMR) AF: 0.514 AC: 7841 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2197 AN: 3470

East Asian (EAS) AF: 0.510 AC: 2647 AN: 5186

South Asian (SAS) AF: 0.449 AC: 2167 AN: 4824

European-Finnish (FIN) AF: 0.425 AC: 4465 AN: 10512

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36806 AN: 67964

Other (OTH) AF: 0.585 AC: 1231 AN: 2104

Alfa AF: 0.549 Hom.: 10888

Bravo AF: 0.591

Asia WGS AF: 0.468 AC: 1622 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.9
DANN	Benign	0.63
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs342758; hg19: chr3-32555180;