chr17-28017473-G-A

Variant names:

• chr17-28017473-G-A
• rs11654637

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 0.0836 in 152,228 control chromosomes in the GnomAD database, including 824 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 0.084 (824 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.339 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: 0.0836 AC: 12721 AN: 152110 Hom.: 823 Cov.: 32

Gnomad AFR AF: 0.0402

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0990

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0737

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0830

Gnomad OTH AF: 0.0905

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

GnomAD4 genome AF: 0.0836 AC: 12726 AN: 152228 Hom.: 824 Cov.: 32 AF XY: 0.0857 AC XY: 6375 AN XY: 74408

African (AFR) AF: 0.0404 AC: 1677 AN: 41548

American (AMR) AF: 0.0988 AC: 1511 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 403 AN: 3472

East Asian (EAS) AF: 0.353 AC: 1825 AN: 5174

South Asian (SAS) AF: 0.133 AC: 643 AN: 4822

European-Finnish (FIN) AF: 0.0737 AC: 781 AN: 10594

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0829 AC: 5640 AN: 68004

Other (OTH) AF: 0.0924 AC: 195 AN: 2110

Alfa AF: 0.0828 Hom.: 111

Bravo AF: 0.0867

Asia WGS AF: 0.228 AC: 793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.66
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs11654637; hg19: chr17-26344499;