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. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.858 AC: 35581 AN: 41488

American (AMR) AF: 0.613 AC: 9372 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1790 AN: 3464

East Asian (EAS) AF: 0.792 AC: 4080 AN: 5152

South Asian (SAS) AF: 0.653 AC: 3130 AN: 4796

European-Finnish (FIN) AF: 0.521 AC: 5497 AN: 10548

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31334 AN: 67958

Other (OTH) AF: 0.571 AC: 1201 AN: 2104

Alfa AF: 0.552 Hom.: 27704

Bravo AF: 0.625

Asia WGS AF: 0.727 AC: 2529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.56
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs2867743; hg19: chr19-32574053;