rs17040246

Variant names:

• chr4-160840524-T-G
• rs17040246

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 0.134 in 151,742 control chromosomes in the GnomAD database, including 1,563 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 0.13 (1563 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20364 AN: 151624 Hom.: 1562 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.0195

Gnomad SAS AF: 0.0678

Gnomad FIN AF: 0.0826

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.134 AC: 20386 AN: 151742 Hom.: 1563 Cov.: 32 AF XY: 0.129 AC XY: 9554 AN XY: 74166

African (AFR) AF: 0.191 AC: 7924 AN: 41452

American (AMR) AF: 0.102 AC: 1560 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 540 AN: 3466

East Asian (EAS) AF: 0.0196 AC: 101 AN: 5166

South Asian (SAS) AF: 0.0682 AC: 329 AN: 4822

European-Finnish (FIN) AF: 0.0826 AC: 874 AN: 10586

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8556 AN: 67706

Other (OTH) AF: 0.128 AC: 270 AN: 2108

Alfa AF: 0.133 Hom.: 2778

Bravo AF: 0.138

Asia WGS AF: 0.0480 AC: 168 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.66
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs17040246; hg19: chr4-161761676;