13-105800628-G-T

Position:

• chr13-105800628-G-T

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 0.81 in 152,016 control chromosomes in the GnomAD database, including 50,424 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 0.81 (50424 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123166 AN: 151898 Hom.: 50427 Cov.: 32

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.810 AC: 123201 AN: 152016 Hom.: 50424 Cov.: 32 AF XY: 0.807 AC XY: 59962 AN XY: 74310

Gnomad4 AFR AF: 0.811

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.826

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.891

Gnomad4 NFE AF: 0.845

Gnomad4 OTH AF: 0.799

Alfa AF: 0.803 Hom.: 30881

Bravo AF: 0.799

Asia WGS AF: 0.703 AC: 2444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.39
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1328083; hg19: chr13-106452977;