rs11125188

chr2-48951297-G-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, non coding transcript 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: ENST00000634588.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.583

Genes affected

(HGNC:):

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000634588.1	n.492+4892G>T		intron_variant, non_coding_transcript_variant		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;