rs11654637

chr17-28017473-G-A

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 0.0836 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0404

Gnomad4 AMR AF: 0.0988

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0737

Gnomad4 NFE AF: 0.0829

Gnomad4 OTH AF: 0.0924

Alfa AF: 0.0831 Hom.: 109

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11654637; hg19: chr17-26344499;