13-31407538-T-C

Position:

• chr13-31407538-T-C

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 0.491 in 151,958 control chromosomes in the GnomAD database, including 19,812 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 0.49 (19812 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74552 AN: 151840 Hom.: 19798 Cov.: 31

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.491 AC: 74590 AN: 151958 Hom.: 19812 Cov.: 31 AF XY: 0.496 AC XY: 36865 AN XY: 74262

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.794

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.540

Alfa AF: 0.533 Hom.: 10573

Bravo AF: 0.496

Asia WGS AF: 0.646 AC: 2244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.2
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1359634; hg19: chr13-31981675;