13-111034262-T-G

Variant names:

• chr13-111034262-T-G
• rs9522088

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 151,780 control chromosomes in the GnomAD database, including 43,639 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 (43639 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.816 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: 113791 AN: 151662 Hom.: 43601 Cov.: 30

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.750 AC: 113885 AN: 151780 Hom.: 43639 Cov.: 30 AF XY: 0.751 AC XY: 55685 AN XY: 74154

African (AFR) AF: 0.599 AC: 24774 AN: 41328

American (AMR) AF: 0.740 AC: 11284 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 2602 AN: 3470

East Asian (EAS) AF: 0.796 AC: 4113 AN: 5164

South Asian (SAS) AF: 0.742 AC: 3550 AN: 4786

European-Finnish (FIN) AF: 0.864 AC: 9104 AN: 10542

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.822 AC: 55823 AN: 67932

Other (OTH) AF: 0.758 AC: 1596 AN: 2106

Alfa AF: 0.797 Hom.: 14730

Bravo AF: 0.734

Asia WGS AF: 0.770 AC: 2679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.7
DANN	Benign	0.45
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs9522088; hg19: chr13-111686609;