ENST00000715414.1:n.502-8674G>A

Variant names:

• chr12-127590937-G-A
• rs2013160
• ENST00000715414.1:n.502-8674G>A

Variant summary

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

The ENST00000715414.1(ENSG00000286922):​n.502-8674G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,924 control chromosomes in the GnomAD database, including 12,891 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 0.41 (12891 hom., cov: 31)
• Consequence: ENSG00000286922 ENST00000715414.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.735
• Publications: 2 publications found

Genes affected

ENSG00000286922 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.442 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
ENSG00000286922	ENST00000715414.1	n.502-8674G>A		intron_variant	Intron 5 of 5
ENSG00000286922	ENST00000715415.1	n.565-8674G>A		intron_variant	Intron 5 of 5
ENSG00000286922	ENST00000776781.1	n.571-8671G>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62092 AN: 151808 Hom.: 12872 Cov.: 31

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.409 AC: 62151 AN: 151924 Hom.: 12891 Cov.: 31 AF XY: 0.414 AC XY: 30757 AN XY: 74250

African (AFR) AF: 0.406 AC: 16819 AN: 41424

American (AMR) AF: 0.390 AC: 5962 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1296 AN: 3470

East Asian (EAS) AF: 0.395 AC: 2031 AN: 5146

South Asian (SAS) AF: 0.458 AC: 2199 AN: 4806

European-Finnish (FIN) AF: 0.545 AC: 5746 AN: 10550

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26730 AN: 67954

Other (OTH) AF: 0.419 AC: 879 AN: 2100

Alfa AF: 0.402 Hom.: 12624

Bravo AF: 0.396

Asia WGS AF: 0.416 AC: 1450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.66
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs2013160; hg19: chr12-128075482;