rs1534401

Positions:

• chr17-43732756-C-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 0.583 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.43732756C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.764

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.571

Alfa AF: 0.621 Hom.: 3688

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1534401; hg19: chr17-41810124;