rs17040246

Variant names:

• chr4-160840524-T-G
• rs17040246

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 0.134 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.134 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

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.0196

Gnomad4 SAS AF: 0.0682

Gnomad4 FIN AF: 0.0826

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.128

Alfa AF: 0.129 Hom.: 1716

Bravo AF: 0.138

Asia WGS AF: 0.0480 AC: 168 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17040246; hg19: chr4-161761676;