rs146026

Positions:

• chr13-32953610-T-C

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 0.75 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.826

Gnomad4 ASJ AF: 0.891

Gnomad4 EAS AF: 0.751

Gnomad4 SAS AF: 0.858

Gnomad4 FIN AF: 0.932

Gnomad4 NFE AF: 0.933

Gnomad4 OTH AF: 0.820

Alfa AF: 0.752 Hom.: 7072

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs146026; hg19: chr13-33527748;