rs17497

Variant names:

• chr11-5036378-C-G
• rs17497

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 0.516 in 151,942 control chromosomes in the GnomAD database, including 20,500 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 0.52 (20500 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.79
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.573 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: 0.515 AC: 78264 AN: 151822 Hom.: 20464 Cov.: 32

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.516 AC: 78345 AN: 151942 Hom.: 20500 Cov.: 32 AF XY: 0.513 AC XY: 38093 AN XY: 74268

African (AFR) AF: 0.579 AC: 24000 AN: 41426

American (AMR) AF: 0.524 AC: 7979 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1888 AN: 3462

East Asian (EAS) AF: 0.263 AC: 1356 AN: 5158

South Asian (SAS) AF: 0.527 AC: 2537 AN: 4814

European-Finnish (FIN) AF: 0.479 AC: 5066 AN: 10568

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33724 AN: 67964

Other (OTH) AF: 0.527 AC: 1113 AN: 2110

Alfa AF: 0.503 Hom.: 2409

Bravo AF: 0.524

Asia WGS AF: 0.414 AC: 1440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.091
DANN	Benign	0.57
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs17497; hg19: chr11-5057608;