chr13-58592441-C-T

Variant names:

• chr13-58592441-C-T
• rs1330748

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 0.161 in 151,974 control chromosomes in the GnomAD database, including 2,481 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 0.16 (2481 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 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: 0.161 AC: 24448 AN: 151856 Hom.: 2484 Cov.: 32

Gnomad AFR AF: 0.0431

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.161 AC: 24443 AN: 151974 Hom.: 2481 Cov.: 32 AF XY: 0.161 AC XY: 11938 AN XY: 74248

African (AFR) AF: 0.0429 AC: 1782 AN: 41516

American (AMR) AF: 0.171 AC: 2599 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1006 AN: 3466

East Asian (EAS) AF: 0.116 AC: 598 AN: 5140

South Asian (SAS) AF: 0.199 AC: 956 AN: 4810

European-Finnish (FIN) AF: 0.202 AC: 2126 AN: 10550

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.217 AC: 14755 AN: 67948

Other (OTH) AF: 0.195 AC: 412 AN: 2110

Alfa AF: 0.180 Hom.: 484

Bravo AF: 0.153

Asia WGS AF: 0.147 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.78
DANN	Benign	0.17
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs1330748; hg19: chr13-59166575;