2-49164883-A-G

Variant names:

• chr2-49164883-A-G
• rs10454135
• ENST00000634588.1:n.492+218478A>G

Variant summary

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

The ENST00000634588.1(ENSG00000282890):​n.492+218478A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 151,882 control chromosomes in the GnomAD database, including 12,369 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 0.39 (12369 hom., cov: 32)
• Consequence: ENSG00000282890 ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 1 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=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.619 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+218478A>G		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59473 AN: 151766 Hom.: 12358 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.392 AC: 59513 AN: 151882 Hom.: 12369 Cov.: 32 AF XY: 0.396 AC XY: 29355 AN XY: 74204

African (AFR) AF: 0.251 AC: 10388 AN: 41398

American (AMR) AF: 0.464 AC: 7083 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1405 AN: 3468

East Asian (EAS) AF: 0.638 AC: 3286 AN: 5154

South Asian (SAS) AF: 0.531 AC: 2555 AN: 4808

European-Finnish (FIN) AF: 0.423 AC: 4451 AN: 10530

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 29017 AN: 67944

Other (OTH) AF: 0.420 AC: 887 AN: 2110

Alfa AF: 0.386 Hom.: 1542

Bravo AF: 0.390

Asia WGS AF: 0.571 AC: 1984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	15
DANN	Benign	0.92
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs10454135; hg19: chr2-49392022;