13-62985342-T-C

Position:

• chr13-62985342-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 0.488 in 151,932 control chromosomes in the GnomAD database, including 19,654 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 (19654 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 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: 0.488 AC: 74087 AN: 151814 Hom.: 19591 Cov.: 31

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.488 AC: 74211 AN: 151932 Hom.: 19654 Cov.: 31 AF XY: 0.496 AC XY: 36835 AN XY: 74264

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.879

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.484

Alfa AF: 0.403 Hom.: 6061

Bravo AF: 0.497

Asia WGS AF: 0.719 AC: 2497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs975423; hg19: chr13-63559475;