chr17-43732756-C-T

Variant names:

• chr17-43732756-C-T
• rs1534401

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 0.583 in 152,132 control chromosomes in the GnomAD database, including 26,730 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 0.58 (26730 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.652 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: 0.583 AC: 88650 AN: 152014 Hom.: 26707 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.583 AC: 88694 AN: 152132 Hom.: 26730 Cov.: 32 AF XY: 0.588 AC XY: 43750 AN XY: 74392

African (AFR) AF: 0.448 AC: 18578 AN: 41482

American (AMR) AF: 0.579 AC: 8835 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2220 AN: 3466

East Asian (EAS) AF: 0.421 AC: 2181 AN: 5182

South Asian (SAS) AF: 0.672 AC: 3240 AN: 4824

European-Finnish (FIN) AF: 0.764 AC: 8080 AN: 10580

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43630 AN: 68010

Other (OTH) AF: 0.571 AC: 1207 AN: 2112

Alfa AF: 0.614 Hom.: 3770

Bravo AF: 0.559

Asia WGS AF: 0.542 AC: 1886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.12
DANN	Benign	0.45
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1534401; hg19: chr17-41810124;