rs17690928

Variant names:

• chr2-64381275-G-A
• rs17690928

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 0.093 in 152,230 control chromosomes in the GnomAD database, including 743 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 0.093 (743 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.112 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: 0.0929 AC: 14136 AN: 152112 Hom.: 743 Cov.: 32

Gnomad AFR AF: 0.0540

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.0929

Gnomad ASJ AF: 0.0554

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.0949

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0842

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

GnomAD4 genome AF: 0.0930 AC: 14153 AN: 152230 Hom.: 743 Cov.: 32 AF XY: 0.0929 AC XY: 6915 AN XY: 74420

Gnomad4 AFR AF: 0.0541

Gnomad4 AMR AF: 0.0929

Gnomad4 ASJ AF: 0.0554

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0962

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.0833

Alfa AF: 0.106 Hom.: 1161

Bravo AF: 0.0858

Asia WGS AF: 0.0610 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17690928; hg19: chr2-64608409;