13-58592441-C-T

Variant names:

• chr13-58592441-C-T
• rs1330748

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 0.161 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.161 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

Gnomad4 AFR AF: 0.0429

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.195

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1330748; hg19: chr13-59166575;