rs12136390

Variant names:

• chr1-181834917-C-T
• rs12136390
• ENST00000717053.1:n.432+575G>A

Variant summary

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

The ENST00000717053.1(ENSG00000287452):​n.432+575G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 151,958 control chromosomes in the GnomAD database, including 4,709 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 0.22 (4709 hom., cov: 32)
• Consequence: ENSG00000287452 ENST00000717053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 2 publications found

Genes affected

ENSG00000287452 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 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
ENSG00000287452	ENST00000717053.1	n.432+575G>A		intron_variant	Intron 2 of 3
ENSG00000287452	ENST00000717054.1	n.437+575G>A		intron_variant	Intron 2 of 3
ENSG00000287452	ENST00000717055.1	n.225+575G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34004 AN: 151840 Hom.: 4698 Cov.: 32

Gnomad AFR AF: 0.0564

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.224 AC: 34025 AN: 151958 Hom.: 4709 Cov.: 32 AF XY: 0.224 AC XY: 16649 AN XY: 74258

African (AFR) AF: 0.0563 AC: 2336 AN: 41490

American (AMR) AF: 0.260 AC: 3972 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1340 AN: 3470

East Asian (EAS) AF: 0.302 AC: 1558 AN: 5166

South Asian (SAS) AF: 0.222 AC: 1062 AN: 4794

European-Finnish (FIN) AF: 0.244 AC: 2570 AN: 10512

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20378 AN: 67932

Other (OTH) AF: 0.234 AC: 494 AN: 2112

Alfa AF: 0.252 Hom.: 760

Bravo AF: 0.217

Asia WGS AF: 0.244 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.5
DANN	Benign	0.83
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs12136390; hg19: chr1-181804052;