ENST00000634588.1:n.492+229135T>C

Variant names:

• chr2-49175540-T-C
• rs1875806
• ENST00000634588.1:n.492+229135T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000634588.1(ENSG00000282890):​n.492+229135T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,038 control chromosomes in the GnomAD database, including 4,252 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 0.23 (4252 hom., cov: 32)
• Consequence: ENSG00000282890 ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110
• Publications: 3 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.286 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+229135T>C		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34286 AN: 151922 Hom.: 4252 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.226 AC: 34291 AN: 152038 Hom.: 4252 Cov.: 32 AF XY: 0.224 AC XY: 16654 AN XY: 74320

African (AFR) AF: 0.128 AC: 5330 AN: 41496

American (AMR) AF: 0.250 AC: 3807 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 734 AN: 3464

East Asian (EAS) AF: 0.227 AC: 1170 AN: 5158

South Asian (SAS) AF: 0.299 AC: 1438 AN: 4808

European-Finnish (FIN) AF: 0.203 AC: 2143 AN: 10572

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.278 AC: 18883 AN: 67980

Other (OTH) AF: 0.209 AC: 442 AN: 2112

Alfa AF: 0.235 Hom.: 599

Bravo AF: 0.223

Asia WGS AF: 0.248 AC: 861 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.44
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs1875806; hg19: chr2-49402679;