rs10490122

Variant names:

• chr2-48897855-G-A
• rs10490122
• ENST00000634588.1:n.303-48361G>A

Variant summary

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

The ENST00000634588.1(ENSG00000282890):​n.303-48361G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0271 in 152,204 control chromosomes in the GnomAD database, including 115 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 0.027 (115 hom., cov: 32)
• Consequence: ENSG00000282890 ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 0 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634588.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000282890	ENST00000634588.1	TSL:5	n.303-48361G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0271 AC: 4114 AN: 152086 Hom.: 113 Cov.: 32

Gnomad AFR AF: 0.00766

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.0184

Gnomad ASJ AF: 0.00750

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.0946

Gnomad FIN AF: 0.0223

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0289

Gnomad OTH AF: 0.0330

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

GnomAD4 genome AF: 0.0271 AC: 4120 AN: 152204 Hom.: 115 Cov.: 32 AF XY: 0.0285 AC XY: 2123 AN XY: 74426

African (AFR) AF: 0.00766 AC: 318 AN: 41526

American (AMR) AF: 0.0184 AC: 281 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00750 AC: 26 AN: 3468

East Asian (EAS) AF: 0.120 AC: 620 AN: 5176

South Asian (SAS) AF: 0.0938 AC: 452 AN: 4818

European-Finnish (FIN) AF: 0.0223 AC: 236 AN: 10602

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0289 AC: 1967 AN: 68002

Other (OTH) AF: 0.0369 AC: 78 AN: 2112

Alfa AF: 0.0242 Hom.: 11

Bravo AF: 0.0260

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.44
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs10490122; hg19: chr2-49124994;