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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.771

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.704

Gnomad4 NFE AF: 0.722

Gnomad4 OTH AF: 0.719

Alfa AF: 0.726 Hom.: 52627

Bravo AF: 0.739

Asia WGS AF: 0.530 AC: 1845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2342371; hg19: chr3-196187608;