13-63328949-T-C

Variant names:

• chr13-63328949-T-C
• rs2992154

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.701 AC: 29006 AN: 41388

American (AMR) AF: 0.776 AC: 11786 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.930 AC: 3220 AN: 3464

East Asian (EAS) AF: 0.925 AC: 4715 AN: 5100

South Asian (SAS) AF: 0.866 AC: 4176 AN: 4824

European-Finnish (FIN) AF: 0.886 AC: 9379 AN: 10586

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.895 AC: 60680 AN: 67832

Other (OTH) AF: 0.854 AC: 1801 AN: 2110

Alfa AF: 0.872 Hom.: 177350

Bravo AF: 0.817

Asia WGS AF: 0.892 AC: 3104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.50
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs2992154; hg19: chr13-63903082;