17-43761526-A-T

Variant names:

• chr17-43761526-A-T
• rs1708635

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 0.63 in 151,588 control chromosomes in the GnomAD database, including 30,427 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 0.63 (30427 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288
• 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 (SAS) allele frequency at 95% confidence interval = 0.647 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: 0.630 AC: 95435 AN: 151470 Hom.: 30386 Cov.: 28

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.630 AC: 95531 AN: 151588 Hom.: 30427 Cov.: 28 AF XY: 0.634 AC XY: 46895 AN XY: 74016

African (AFR) AF: 0.643 AC: 26525 AN: 41258

American (AMR) AF: 0.568 AC: 8660 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2160 AN: 3472

East Asian (EAS) AF: 0.347 AC: 1768 AN: 5098

South Asian (SAS) AF: 0.666 AC: 3203 AN: 4808

European-Finnish (FIN) AF: 0.749 AC: 7862 AN: 10494

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43391 AN: 67900

Other (OTH) AF: 0.600 AC: 1264 AN: 2106

Alfa AF: 0.540 Hom.: 1517

Bravo AF: 0.612

Asia WGS AF: 0.522 AC: 1816 AN: 3476

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	0.80
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1708635; hg19: chr17-41838894;