13-105381034-C-T

Variant names:

• chr13-105381034-C-T
• rs1570709

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 0.785 in 152,164 control chromosomes in the GnomAD database, including 47,088 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 0.78 (47088 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 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: 0.785 AC: 119302 AN: 152046 Hom.: 47051 Cov.: 32

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.785 AC: 119392 AN: 152164 Hom.: 47088 Cov.: 32 AF XY: 0.783 AC XY: 58228 AN XY: 74384

African (AFR) AF: 0.824 AC: 34227 AN: 41514

American (AMR) AF: 0.714 AC: 10914 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2881 AN: 3472

East Asian (EAS) AF: 0.576 AC: 2974 AN: 5166

South Asian (SAS) AF: 0.731 AC: 3516 AN: 4812

European-Finnish (FIN) AF: 0.820 AC: 8686 AN: 10594

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.787 AC: 53535 AN: 68012

Other (OTH) AF: 0.777 AC: 1638 AN: 2108

Alfa AF: 0.780 Hom.: 106373

Bravo AF: 0.775

Asia WGS AF: 0.684 AC: 2382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.74
DANN	Benign	0.39
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1570709; hg19: chr13-106033384;