rs11125188

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000282890 (HGNC:58158):

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.427

Alfa AF: 0.454 Hom.: 20478

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11125188; hg19: chr2-49178436;