rs2867743

Variant names:

• chr19-32083147-A-G
• rs2867743

Your query was ambiguous. Multiple possible variants found:

• chr19-32083147-A-G
• chr19-32083147-A-T

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 0.609 in 152,000 control chromosomes in the GnomAD database, including 30,577 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 0.61 (30577 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 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: 0.609 AC: 92437 AN: 151882 Hom.: 30510 Cov.: 32

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.609 AC: 92564 AN: 152000 Hom.: 30577 Cov.: 32 AF XY: 0.613 AC XY: 45529 AN XY: 74284

Gnomad4 AFR AF: 0.858

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.571

Alfa AF: 0.519 Hom.: 14259

Bravo AF: 0.625

Asia WGS AF: 0.727 AC: 2529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2867743; hg19: chr19-32574053;