ENST00000634588.1:n.492+4057C>T

Variant names:

• chr2-48950462-C-T
• rs7591064
• ENST00000634588.1:n.492+4057C>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+4057C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.86 in 152,228 control chromosomes in the GnomAD database, including 56,746 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 0.86 (56746 hom., cov: 32)
• Consequence: ENSG00000282890 ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443
• Publications: 8 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634588.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000282890	ENST00000634588.1	TSL:5	n.492+4057C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.860 AC: 130867 AN: 152110 Hom.: 56687 Cov.: 32

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.860 AC: 130981 AN: 152228 Hom.: 56746 Cov.: 32 AF XY: 0.862 AC XY: 64160 AN XY: 74448

African (AFR) AF: 0.953 AC: 39574 AN: 41528

American (AMR) AF: 0.867 AC: 13272 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2596 AN: 3468

East Asian (EAS) AF: 0.943 AC: 4885 AN: 5180

South Asian (SAS) AF: 0.802 AC: 3862 AN: 4814

European-Finnish (FIN) AF: 0.858 AC: 9103 AN: 10608

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55058 AN: 68010

Other (OTH) AF: 0.834 AC: 1762 AN: 2112

Alfa AF: 0.824 Hom.: 187885

Bravo AF: 0.866

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.21
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs7591064; hg19: chr2-49177601;