rs1756091

Variant names:

• chr13-111567506-A-C
• rs1756091

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 0.853 in 152,162 control chromosomes in the GnomAD database, including 55,688 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 0.85 (55688 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 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: 0.853 AC: 129720 AN: 152044 Hom.: 55651 Cov.: 33

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.865

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

GnomAD4 genome AF: 0.853 AC: 129815 AN: 152162 Hom.: 55688 Cov.: 33 AF XY: 0.859 AC XY: 63885 AN XY: 74384

African (AFR) AF: 0.764 AC: 31687 AN: 41472

American (AMR) AF: 0.900 AC: 13768 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3053 AN: 3470

East Asian (EAS) AF: 0.964 AC: 4990 AN: 5176

South Asian (SAS) AF: 0.914 AC: 4404 AN: 4820

European-Finnish (FIN) AF: 0.933 AC: 9897 AN: 10610

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.870 AC: 59134 AN: 67998

Other (OTH) AF: 0.864 AC: 1826 AN: 2114

Alfa AF: 0.863 Hom.: 193391

Bravo AF: 0.846

Asia WGS AF: 0.921 AC: 3204 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	2.3
DANN	Benign	0.50
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1756091; hg19: chr13-112219853;