2-48815260-A-T

Variant names:

• chr2-48815260-A-T
• rs9636432
• ENST00000634588.1:n.302+5619A>T

Variant summary

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

The ENST00000634588.1(ENSG00000282890):​n.302+5619A>T 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 152,120 control chromosomes in the GnomAD database, including 5,021 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 (5021 hom., cov: 32)
• Consequence: ENSG00000282890 ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 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+5619A>T		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34373 AN: 152002 Hom.: 5030 Cov.: 32

Gnomad AFR AF: 0.0580

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.226 AC: 34358 AN: 152120 Hom.: 5021 Cov.: 32 AF XY: 0.232 AC XY: 17238 AN XY: 74346

African (AFR) AF: 0.0579 AC: 2406 AN: 41546

American (AMR) AF: 0.204 AC: 3111 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1129 AN: 3470

East Asian (EAS) AF: 0.574 AC: 2968 AN: 5170

South Asian (SAS) AF: 0.317 AC: 1529 AN: 4822

European-Finnish (FIN) AF: 0.321 AC: 3403 AN: 10590

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19120 AN: 67986

Other (OTH) AF: 0.230 AC: 486 AN: 2116

Alfa AF: 0.104 Hom.: 183

Bravo AF: 0.208

Asia WGS AF: 0.385 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.020
DANN	Benign	0.60
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs9636432; hg19: chr2-49042399;