rs2342371

Variant names:

• chr3-196460737-G-A
• rs2342371

Your query was ambiguous. Multiple possible variants found:

• chr3-196460737-G-A
• chr3-196460737-G-C

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 0.739 in 152,026 control chromosomes in the GnomAD database, including 42,454 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 (42454 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 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: 0.739 AC: 112299 AN: 151908 Hom.: 42422 Cov.: 31

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.739 AC: 112383 AN: 152026 Hom.: 42454 Cov.: 31 AF XY: 0.734 AC XY: 54559 AN XY: 74316

African (AFR) AF: 0.860 AC: 35680 AN: 41492

American (AMR) AF: 0.664 AC: 10125 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 2674 AN: 3466

East Asian (EAS) AF: 0.274 AC: 1417 AN: 5168

South Asian (SAS) AF: 0.725 AC: 3496 AN: 4822

European-Finnish (FIN) AF: 0.704 AC: 7423 AN: 10546

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.722 AC: 49074 AN: 67970

Other (OTH) AF: 0.719 AC: 1512 AN: 2102

Alfa AF: 0.737 Hom.: 93702

Bravo AF: 0.739

Asia WGS AF: 0.530 AC: 1845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.22
DANN	Benign	0.65
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2342371; hg19: chr3-196187608;