rs2013160

Variant names:

• chr12-127590937-G-A
• rs2013160
• ENST00000660759.1:n.*7G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000660759.1(ENSG00000287622):​n.*7G>A variant causes a downstream gene 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: ENSG00000287622 ENST00000660759.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.735

Genes affected

ENSG00000287622 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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
ENSG00000287622	ENST00000660759.1	n.*7G>A		downstream_gene_variant

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

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.419

Alfa AF: 0.404 Hom.: 6885

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2013160; hg19: chr12-128075482;