chr13-24606013-C-T

Variant names:

• chr13-24606013-C-T
• rs943049

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 0.448 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.433

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.418

Alfa AF: 0.452 Hom.: 11049

Bravo AF: 0.455

Asia WGS AF: 0.492 AC: 1712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs943049; hg19: chr13-25180151;