rs17497

chr11-5036378-C-G

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 0.516 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.579

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.527

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17497; hg19: chr11-5057608;