rs11125188

Variant names:

• chr2-48951297-G-T
• rs11125188
• ENST00000634588.1:n.492+4892G>T

Variant summary

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

The ENST00000634588.1(ENSG00000282890):​n.492+4892G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 152,020 control chromosomes in the GnomAD database, including 14,859 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 0.44 (14859 hom., cov: 32)
• Consequence: ENSG00000282890 ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.583
• Publications: 1 publications found

Genes affected

ENSG00000282890 (HGNC:58158):

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 (SAS) allele frequency at 95% confidence interval = 0.456 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
ENSG00000282890	ENST00000634588.1	n.492+4892G>T		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66927 AN: 151902 Hom.: 14853 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.440 AC: 66960 AN: 152020 Hom.: 14859 Cov.: 32 AF XY: 0.440 AC XY: 32669 AN XY: 74308

African (AFR) AF: 0.410 AC: 17003 AN: 41456

American (AMR) AF: 0.453 AC: 6919 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1354 AN: 3472

East Asian (EAS) AF: 0.404 AC: 2089 AN: 5170

South Asian (SAS) AF: 0.471 AC: 2272 AN: 4822

European-Finnish (FIN) AF: 0.445 AC: 4692 AN: 10542

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31311 AN: 67972

Other (OTH) AF: 0.427 AC: 901 AN: 2108

Alfa AF: 0.452 Hom.: 25833

Bravo AF: 0.436

Asia WGS AF: 0.444 AC: 1546 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	0.66
DANN	Benign	0.26
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs11125188; hg19: chr2-49178436;