rs1756091

Positions:

• chr13-111567506-A-C

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 0.853 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.900

Gnomad4 ASJ AF: 0.880

Gnomad4 EAS AF: 0.964

Gnomad4 SAS AF: 0.914

Gnomad4 FIN AF: 0.933

Gnomad4 NFE AF: 0.870

Gnomad4 OTH AF: 0.864

Alfa AF: 0.867 Hom.: 70274

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1756091; hg19: chr13-112219853;