13-111921290-A-T

Variant names:

• chr13-111921290-A-T
• rs9577381

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 0.671 in 152,136 control chromosomes in the GnomAD database, including 34,380 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 0.67 (34380 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.688 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: 0.672 AC: 102087 AN: 152018 Hom.: 34370 Cov.: 33

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.671 AC: 102139 AN: 152136 Hom.: 34380 Cov.: 33 AF XY: 0.665 AC XY: 49460 AN XY: 74366

African (AFR) AF: 0.675 AC: 28010 AN: 41498

American (AMR) AF: 0.635 AC: 9703 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2214 AN: 3470

East Asian (EAS) AF: 0.520 AC: 2681 AN: 5158

South Asian (SAS) AF: 0.701 AC: 3385 AN: 4830

European-Finnish (FIN) AF: 0.636 AC: 6730 AN: 10580

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47130 AN: 67992

Other (OTH) AF: 0.687 AC: 1453 AN: 2116

Alfa AF: 0.671 Hom.: 4036

Bravo AF: 0.673

Asia WGS AF: 0.603 AC: 2098 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	0.27
DANN	Benign	0.38
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs9577381; hg19: chr13-112575604;