XR_001750032.2:n.595-15366T>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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984618	XR_001750032.2	n.595-15366T>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;