13-74597003-C-T

Variant names:

• chr13-74597003-C-T
• rs9318293

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 0.632 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.632 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

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.623

Alfa AF: 0.679 Hom.: 71462

Bravo AF: 0.625

Asia WGS AF: 0.615 AC: 2139 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9318293; hg19: chr13-75171140;