rs17483987

Variant names:

• chr2-48863314-C-T
• rs17483987
• ENST00000634588.1:n.302+53673C>T

Variant summary

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

The ENST00000634588.1(ENSG00000282890):​n.302+53673C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,190 control chromosomes in the GnomAD database, including 1,203 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 0.11 (1203 hom., cov: 33)
• Consequence: ENSG00000282890 ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992

Genes affected

ENSG00000282890 (HGNC:58158):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.163 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.302+53673C>T		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16944 AN: 152072 Hom.: 1204 Cov.: 33

Gnomad AFR AF: 0.0378

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0950

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.111 AC: 16933 AN: 152190 Hom.: 1203 Cov.: 33 AF XY: 0.115 AC XY: 8540 AN XY: 74418

Gnomad4 AFR AF: 0.0378

Gnomad4 AMR AF: 0.0949

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.115

Alfa AF: 0.117 Hom.: 151

Bravo AF: 0.102

Asia WGS AF: 0.127 AC: 441 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.90
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17483987; hg19: chr2-49090453;