ENST00000458480.2:n.48+11407G>A

Variant names:

• chr13-81261892-G-A
• rs1287526
• ENST00000458480.2:n.48+11407G>A

Variant summary

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

The ENST00000458480.2(ENSG00000229309):​n.48+11407G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 150,194 control chromosomes in the GnomAD database, including 53,630 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 0.84 (53630 hom., cov: 27)
• Consequence: ENSG00000229309 ENST00000458480.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244
• Publications: 3 publications found

Genes affected

ENSG00000229309 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229309	ENST00000458480.2	n.48+11407G>A		intron_variant	Intron 1 of 5	3
ENSG00000229309	ENST00000782961.1	n.71+11407G>A		intron_variant	Intron 1 of 4
ENSG00000229309	ENST00000782962.1	n.126+11407G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.844 AC: 126721 AN: 150090 Hom.: 53606 Cov.: 27

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.735

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.844 AC: 126792 AN: 150194 Hom.: 53630 Cov.: 27 AF XY: 0.843 AC XY: 61713 AN XY: 73244

African (AFR) AF: 0.804 AC: 32872 AN: 40896

American (AMR) AF: 0.837 AC: 12608 AN: 15056

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2808 AN: 3450

East Asian (EAS) AF: 0.698 AC: 3553 AN: 5092

South Asian (SAS) AF: 0.798 AC: 3796 AN: 4754

European-Finnish (FIN) AF: 0.896 AC: 9000 AN: 10050

Middle Eastern (MID) AF: 0.719 AC: 207 AN: 288

European-Non Finnish (NFE) AF: 0.879 AC: 59440 AN: 67600

Other (OTH) AF: 0.811 AC: 1700 AN: 2096

Alfa AF: 0.869 Hom.: 70499

Bravo AF: 0.838

Asia WGS AF: 0.727 AC: 2523 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.12
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs1287526; hg19: chr13-81836027;