rs146026

Variant names:

• chr13-32953610-T-C
• rs146026

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 0.75 in 151,832 control chromosomes in the GnomAD database, including 47,710 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 0.75 (47710 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.927 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: 0.750 AC: 113855 AN: 151718 Hom.: 47715 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.866

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.750 AC: 113868 AN: 151832 Hom.: 47710 Cov.: 32 AF XY: 0.753 AC XY: 55892 AN XY: 74220

African (AFR) AF: 0.341 AC: 14121 AN: 41426

American (AMR) AF: 0.826 AC: 12599 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.891 AC: 3085 AN: 3462

East Asian (EAS) AF: 0.751 AC: 3847 AN: 5122

South Asian (SAS) AF: 0.858 AC: 4131 AN: 4812

European-Finnish (FIN) AF: 0.932 AC: 9888 AN: 10608

Middle Eastern (MID) AF: 0.863 AC: 252 AN: 292

European-Non Finnish (NFE) AF: 0.933 AC: 63341 AN: 67856

Other (OTH) AF: 0.820 AC: 1726 AN: 2104

Alfa AF: 0.741 Hom.: 25764

Bravo AF: 0.723

Asia WGS AF: 0.764 AC: 2656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.28
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs146026; hg19: chr13-33527748;