rs17090640

Variant names:

• chr4-179746494-G-A
• rs17090640

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 0.107 in 151,950 control chromosomes in the GnomAD database, including 1,648 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 0.11 (1648 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.953
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 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: 0.107 AC: 16229 AN: 151832 Hom.: 1647 Cov.: 31

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.0641

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0547

Gnomad FIN AF: 0.0172

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0477

Gnomad OTH AF: 0.0943

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

GnomAD4 genome AF: 0.107 AC: 16247 AN: 151950 Hom.: 1648 Cov.: 31 AF XY: 0.103 AC XY: 7646 AN XY: 74258

African (AFR) AF: 0.269 AC: 11109 AN: 41364

American (AMR) AF: 0.0639 AC: 974 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3468

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5170

South Asian (SAS) AF: 0.0549 AC: 264 AN: 4808

European-Finnish (FIN) AF: 0.0172 AC: 182 AN: 10592

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0476 AC: 3239 AN: 67980

Other (OTH) AF: 0.0934 AC: 197 AN: 2110

Alfa AF: 0.0693 Hom.: 2173

Bravo AF: 0.117

Asia WGS AF: 0.0380 AC: 132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.016
DANN	Benign	0.70
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs17090640; hg19: chr4-180667647;