ENST00000515296.1:n.182-17050T>A

Variant names:

• chr5-139704853-T-A
• rs356484
• ENST00000515296.1:n.182-17050T>A

Variant summary

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

The ENST00000515296.1(ENSG00000249526):​n.182-17050T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 151,916 control chromosomes in the GnomAD database, including 5,719 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 0.27 (5719 hom., cov: 31)
• Consequence: ENSG00000249526 ENST00000515296.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576
• Publications: 3 publications found

Genes affected

ENSG00000249526 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.327 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
ENSG00000249526	ENST00000515296.1	n.182-17050T>A		intron_variant	Intron 2 of 5	4

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40669 AN: 151798 Hom.: 5713 Cov.: 31

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0660

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.268 AC: 40698 AN: 151916 Hom.: 5719 Cov.: 31 AF XY: 0.264 AC XY: 19574 AN XY: 74238

African (AFR) AF: 0.332 AC: 13728 AN: 41408

American (AMR) AF: 0.230 AC: 3506 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 798 AN: 3470

East Asian (EAS) AF: 0.0661 AC: 341 AN: 5156

South Asian (SAS) AF: 0.141 AC: 675 AN: 4798

European-Finnish (FIN) AF: 0.249 AC: 2635 AN: 10562

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18072 AN: 67948

Other (OTH) AF: 0.286 AC: 604 AN: 2112

Alfa AF: 0.134 Hom.: 231

Bravo AF: 0.270

Asia WGS AF: 0.151 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.52
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs356484; hg19: chr5-139084438;