13-74597003-C-T

Variant names:

• chr13-74597003-C-T
• rs9318293

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 0.632 in 152,036 control chromosomes in the GnomAD database, including 31,055 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 0.63 (31055 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.688 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: 0.632 AC: 96055 AN: 151918 Hom.: 31039 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.632 AC: 96110 AN: 152036 Hom.: 31055 Cov.: 32 AF XY: 0.635 AC XY: 47177 AN XY: 74312

African (AFR) AF: 0.485 AC: 20092 AN: 41450

American (AMR) AF: 0.696 AC: 10634 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2139 AN: 3472

East Asian (EAS) AF: 0.657 AC: 3389 AN: 5156

South Asian (SAS) AF: 0.658 AC: 3166 AN: 4812

European-Finnish (FIN) AF: 0.718 AC: 7588 AN: 10574

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.693 AC: 47141 AN: 67976

Other (OTH) AF: 0.623 AC: 1311 AN: 2106

Alfa AF: 0.669 Hom.: 107331

Bravo AF: 0.625

Asia WGS AF: 0.615 AC: 2139 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.18
DANN	Benign	0.58
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs9318293; hg19: chr13-75171140;