13-63328949-T-C

Position:

• chr13-63328949-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 0.83 in 151,694 control chromosomes in the GnomAD database, including 52,843 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 0.83 (52843 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.830 AC: 125828 AN: 151576 Hom.: 52825 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.951

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.830 AC: 125894 AN: 151694 Hom.: 52843 Cov.: 32 AF XY: 0.830 AC XY: 61508 AN XY: 74150

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.776

Gnomad4 ASJ AF: 0.930

Gnomad4 EAS AF: 0.925

Gnomad4 SAS AF: 0.866

Gnomad4 FIN AF: 0.886

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.854

Alfa AF: 0.886 Hom.: 116728

Bravo AF: 0.817

Asia WGS AF: 0.892 AC: 3104 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	0.45
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2992154; hg19: chr13-63903082;