17-43761526-A-T

Position:

• chr17-43761526-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 0.63 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

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 (SAS) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.600

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1708635; hg19: chr17-41838894;