13-26841536-A-T

Variant names:

• chr13-26841536-A-T
• rs9319321

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 0.758 in 152,108 control chromosomes in the GnomAD database, including 44,406 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 0.76 (44406 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.866 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: 0.758 AC: 115272 AN: 151990 Hom.: 44364 Cov.: 31

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.758 AC: 115361 AN: 152108 Hom.: 44406 Cov.: 31 AF XY: 0.746 AC XY: 55458 AN XY: 74340

Gnomad4 AFR AF: 0.874

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.769

Alfa AF: 0.736 Hom.: 19907

Bravo AF: 0.766

Asia WGS AF: 0.608 AC: 2113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.014
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9319321; hg19: chr13-27415673;