chr13-26947673-A-G

Position:

• chr13-26947673-A-G

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 0.093 in 152,266 control chromosomes in the GnomAD database, including 753 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 0.093 (753 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0982 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: 0.0930 AC: 14145 AN: 152148 Hom.: 753 Cov.: 32

Gnomad AFR AF: 0.0948

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0612

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0454

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0743

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

GnomAD4 genome AF: 0.0930 AC: 14157 AN: 152266 Hom.: 753 Cov.: 32 AF XY: 0.0930 AC XY: 6921 AN XY: 74448

Gnomad4 AFR AF: 0.0949

Gnomad4 AMR AF: 0.0612

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0452

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.0735

Alfa AF: 0.0961 Hom.: 961

Bravo AF: 0.0858

Asia WGS AF: 0.0270 AC: 92 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7326591; hg19: chr13-27521810;