13-44760058-C-T

Variant names:

• chr13-44760058-C-T
• rs9533962

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 0.474 in 151,786 control chromosomes in the GnomAD database, including 18,787 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 0.47 (18787 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.758
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.588 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: 0.474 AC: 71945 AN: 151668 Hom.: 18788 Cov.: 30

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.474 AC: 71949 AN: 151786 Hom.: 18787 Cov.: 30 AF XY: 0.471 AC XY: 34929 AN XY: 74176

African (AFR) AF: 0.246 AC: 10166 AN: 41374

American (AMR) AF: 0.455 AC: 6924 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2237 AN: 3468

East Asian (EAS) AF: 0.545 AC: 2805 AN: 5150

South Asian (SAS) AF: 0.461 AC: 2214 AN: 4806

European-Finnish (FIN) AF: 0.527 AC: 5551 AN: 10524

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.593 AC: 40253 AN: 67916

Other (OTH) AF: 0.497 AC: 1051 AN: 2114

Alfa AF: 0.558 Hom.: 34374

Bravo AF: 0.461

Asia WGS AF: 0.431 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.1
DANN	Benign	0.48
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs9533962; hg19: chr13-45334194;