13-111435586-T-A

Variant names:

• chr13-111435586-T-A
• rs1163849
• XR_001750032.2:n.595-15366T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001750032.2(LOC107984618):​n.595-15366T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.828 in 152,062 control chromosomes in the GnomAD database, including 53,478 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 0.83 (53478 hom., cov: 31)
• Consequence: LOC107984618 XR_001750032.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 0 publications found

Genes affected

LOC107984618 (HGNC:):

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 = 0.902 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.829 AC: 125891 AN: 151944 Hom.: 53456 Cov.: 31

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.911

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.949

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.828 AC: 125962 AN: 152062 Hom.: 53478 Cov.: 31 AF XY: 0.834 AC XY: 61962 AN XY: 74334

African (AFR) AF: 0.616 AC: 25516 AN: 41392

American (AMR) AF: 0.895 AC: 13679 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.911 AC: 3160 AN: 3470

East Asian (EAS) AF: 0.897 AC: 4641 AN: 5172

South Asian (SAS) AF: 0.887 AC: 4277 AN: 4824

European-Finnish (FIN) AF: 0.949 AC: 10068 AN: 10604

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.908 AC: 61719 AN: 67994

Other (OTH) AF: 0.833 AC: 1760 AN: 2114

Alfa AF: 0.858 Hom.: 7057

Bravo AF: 0.815

Asia WGS AF: 0.855 AC: 2968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.22
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1163849; hg19: chr13-112087933;