rs11617463

chr13-74756956-C-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 0.0673 in 152,214 control chromosomes in the GnomAD database, including 460 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 0.067 (460 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.618

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 (SAS) allele frequency at 95% confidence interval = 0.145 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: 0.0673 AC: 10242 AN: 152096 Hom.: 460 Cov.: 33

Gnomad AFR AF: 0.0214

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.0682

Gnomad ASJ AF: 0.0862

Gnomad EAS AF: 0.0398

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0810

Gnomad OTH AF: 0.0511

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

GnomAD4 genome AF: 0.0673 AC: 10243 AN: 152214 Hom.: 460 Cov.: 33 AF XY: 0.0701 AC XY: 5217 AN XY: 74434

Gnomad4 AFR AF: 0.0213

Gnomad4 AMR AF: 0.0682

Gnomad4 ASJ AF: 0.0862

Gnomad4 EAS AF: 0.0401

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.0810

Gnomad4 OTH AF: 0.0520

Alfa AF: 0.0832 Hom.: 369

Bravo AF: 0.0579

Asia WGS AF: 0.107 AC: 371 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	0.48
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11617463; hg19: chr13-75331093; COSMIC: COSV69364637;