rs953360

Positions:

• chr13-111522232-G-A

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 0.0757 in 152,266 control chromosomes in the GnomAD database, including 613 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 0.076 (613 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.111522232G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0758 AC: 11530 AN: 152148 Hom.: 615 Cov.: 33

Gnomad AFR AF: 0.0449

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.0782

Gnomad ASJ AF: 0.0594

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0664

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0766

Gnomad OTH AF: 0.0654

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

GnomAD4 genome AF: 0.0757 AC: 11534 AN: 152266 Hom.: 613 Cov.: 33 AF XY: 0.0776 AC XY: 5779 AN XY: 74460

Gnomad4 AFR AF: 0.0450

Gnomad4 AMR AF: 0.0780

Gnomad4 ASJ AF: 0.0594

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0664

Gnomad4 NFE AF: 0.0766

Gnomad4 OTH AF: 0.0638

Alfa AF: 0.0772 Hom.: 282

Bravo AF: 0.0751

Asia WGS AF: 0.178 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.11
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs953360; hg19: chr13-112174579;