rs17404262

Variant names:

• chr15-49675422-A-G
• rs17404262

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 0.176 in 151,792 control chromosomes in the GnomAD database, including 3,043 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 0.18 (3043 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.243 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: 0.177 AC: 26804 AN: 151674 Hom.: 3046 Cov.: 32

Gnomad AFR AF: 0.0443

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.00427

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.176 AC: 26789 AN: 151792 Hom.: 3043 Cov.: 32 AF XY: 0.179 AC XY: 13251 AN XY: 74180

Gnomad4 AFR AF: 0.0442

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.00448

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.192

Alfa AF: 0.214 Hom.: 512

Bravo AF: 0.160

Asia WGS AF: 0.0760 AC: 262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.49
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17404262; hg19: chr15-49967619;