rs12130868

Variant names:

• chr1-181819078-C-T
• rs12130868
• ENST00000717053.1:n.433-8135G>A

Variant summary

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

The ENST00000717053.1(ENSG00000287452):​n.433-8135G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,068 control chromosomes in the GnomAD database, including 4,749 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 0.23 (4749 hom., cov: 32)
• Consequence: ENSG00000287452 ENST00000717053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 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.433-8135G>A		intron_variant	Intron 2 of 3
ENSG00000287452	ENST00000717054.1	n.438-8115G>A		intron_variant	Intron 2 of 3
ENSG00000287452	ENST00000717055.1	n.226-8115G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34502 AN: 151950 Hom.: 4738 Cov.: 32

Gnomad AFR AF: 0.0678

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.245

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: 0.227 AC: 34523 AN: 152068 Hom.: 4749 Cov.: 32 AF XY: 0.227 AC XY: 16895 AN XY: 74322

African (AFR) AF: 0.0677 AC: 2809 AN: 41514

American (AMR) AF: 0.261 AC: 3979 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1341 AN: 3472

East Asian (EAS) AF: 0.301 AC: 1551 AN: 5150

South Asian (SAS) AF: 0.223 AC: 1074 AN: 4816

European-Finnish (FIN) AF: 0.245 AC: 2590 AN: 10582

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

European-Non Finnish (NFE) AF: 0.300 AC: 20370 AN: 67944

Other (OTH) AF: 0.234 AC: 494 AN: 2114

Alfa AF: 0.251 Hom.: 1074

Bravo AF: 0.220

Asia WGS AF: 0.246 AC: 857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.42
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs12130868; hg19: chr1-181788213;