chr13-74756956-C-A

Variant names:

• chr13-74756956-C-A
• rs11617463

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 0.0673 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
• Publications: 3 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 (SAS) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0213 AC: 886 AN: 41540

American (AMR) AF: 0.0682 AC: 1042 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0862 AC: 299 AN: 3470

East Asian (EAS) AF: 0.0401 AC: 208 AN: 5188

South Asian (SAS) AF: 0.154 AC: 741 AN: 4812

European-Finnish (FIN) AF: 0.130 AC: 1381 AN: 10588

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0810 AC: 5508 AN: 68010

Other (OTH) AF: 0.0520 AC: 110 AN: 2114

Alfa AF: 0.0818 Hom.: 491

Bravo AF: 0.0579

Asia WGS AF: 0.107 AC: 371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.48
DANN	Benign	0.40
PhyloP100		-0.62

Splicing

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

Other links and lift over

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