chr13-111522232-G-A

Variant names:

• chr13-111522232-G-A
• rs953360

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 0.0757 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 2 publications found

ACMG classification

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

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

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0450 AC: 1869 AN: 41558

American (AMR) AF: 0.0780 AC: 1194 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0594 AC: 206 AN: 3470

East Asian (EAS) AF: 0.299 AC: 1541 AN: 5162

South Asian (SAS) AF: 0.117 AC: 565 AN: 4826

European-Finnish (FIN) AF: 0.0664 AC: 705 AN: 10616

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0766 AC: 5212 AN: 68008

Other (OTH) AF: 0.0638 AC: 135 AN: 2116

Alfa AF: 0.0799 Hom.: 542

Bravo AF: 0.0751

Asia WGS AF: 0.178 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.11
DANN	Benign	0.48
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs953360; hg19: chr13-112174579;