13-24606013-C-T

Variant names:

• chr13-24606013-C-T
• rs943049

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 0.448 in 152,052 control chromosomes in the GnomAD database, including 15,389 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 0.45 (15389 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.574 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: 0.448 AC: 68112 AN: 151934 Hom.: 15375 Cov.: 33

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.448 AC: 68162 AN: 152052 Hom.: 15389 Cov.: 33 AF XY: 0.451 AC XY: 33544 AN XY: 74322

African (AFR) AF: 0.433 AC: 17958 AN: 41490

American (AMR) AF: 0.503 AC: 7690 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1630 AN: 3470

East Asian (EAS) AF: 0.476 AC: 2458 AN: 5162

South Asian (SAS) AF: 0.592 AC: 2846 AN: 4810

European-Finnish (FIN) AF: 0.396 AC: 4180 AN: 10564

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29860 AN: 67964

Other (OTH) AF: 0.418 AC: 881 AN: 2106

Alfa AF: 0.450 Hom.: 12757

Bravo AF: 0.455

Asia WGS AF: 0.492 AC: 1712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.8
DANN	Benign	0.90
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs943049; hg19: chr13-25180151;