rs2342371

chr3-196460737-G-Achr3-196460737-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;