2-48950462-C-T

Variant names:

• chr2-48950462-C-T
• rs7591064
• ENST00000634588.1:n.492+4057C>T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000282890 (HGNC:58158):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.945 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+4057C>T		intron_variant	Intron 2 of 4	5

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

Gnomad4 AFR AF: 0.953

Gnomad4 AMR AF: 0.867

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.802

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.834

Alfa AF: 0.814 Hom.: 79256

Bravo AF: 0.866

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7591064; hg19: chr2-49177601;