13-105800628-G-T

Variant names:

• chr13-105800628-G-T
• rs1328083

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 0.81 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.811 AC: 33642 AN: 41480

American (AMR) AF: 0.675 AC: 10284 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2683 AN: 3470

East Asian (EAS) AF: 0.826 AC: 4237 AN: 5132

South Asian (SAS) AF: 0.564 AC: 2715 AN: 4814

European-Finnish (FIN) AF: 0.891 AC: 9452 AN: 10604

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.845 AC: 57449 AN: 67972

Other (OTH) AF: 0.799 AC: 1684 AN: 2108

Alfa AF: 0.812 Hom.: 44031

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
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1328083; hg19: chr13-106452977;