ENST00000634588.1:n.303-38842C>T

Variant names:

• chr2-48907374-C-T
• rs2215911
• ENST00000634588.1:n.303-38842C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000634588.1(ENSG00000282890):​n.303-38842C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 152,038 control chromosomes in the GnomAD database, including 25,332 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 0.57 (25332 hom., cov: 32)
• Consequence: ENSG00000282890 ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488

Genes affected

ENSG00000282890 (HGNC:58158):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 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.303-38842C>T		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86924 AN: 151920 Hom.: 25298 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.572 AC: 87010 AN: 152038 Hom.: 25332 Cov.: 32 AF XY: 0.581 AC XY: 43153 AN XY: 74304

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.799

Gnomad4 SAS AF: 0.575

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.572

Alfa AF: 0.528 Hom.: 9776

Bravo AF: 0.585

Asia WGS AF: 0.703 AC: 2445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.54
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2215911; hg19: chr2-49134513;