13-31333604-C-T

Position:

• chr13-31333604-C-T

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 0.665 in 151,888 control chromosomes in the GnomAD database, including 34,790 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 0.66 (34790 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.31333604C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.665 AC: 100959 AN: 151770 Hom.: 34789 Cov.: 31

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.665 AC: 101002 AN: 151888 Hom.: 34790 Cov.: 31 AF XY: 0.660 AC XY: 49055 AN XY: 74270

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.757

Gnomad4 EAS AF: 0.572

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.766

Gnomad4 OTH AF: 0.671

Alfa AF: 0.732 Hom.: 18523

Bravo AF: 0.658

Asia WGS AF: 0.625 AC: 2172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.38
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1409379; hg19: chr13-31907741;