rs10490125

Positions:

• chr2-48897059-T-A
• chr2-48897059-T-G

Variant summary

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

The variant allele was found at a frequency of 0.027 in 152,318 control chromosomes in the GnomAD database, including 117 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 (117 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.48897059T>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000282890	ENST00000634588.1	n.303-49157T>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0269 AC: 4098 AN: 152200 Hom.: 114 Cov.: 32

Gnomad AFR AF: 0.00765

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.0185

Gnomad ASJ AF: 0.00606

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.0891

Gnomad FIN AF: 0.0222

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0290

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0270 AC: 4105 AN: 152318 Hom.: 117 Cov.: 32 AF XY: 0.0284 AC XY: 2114 AN XY: 74488

Gnomad4 AFR AF: 0.00765

Gnomad4 AMR AF: 0.0184

Gnomad4 ASJ AF: 0.00606

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.0883

Gnomad4 FIN AF: 0.0222

Gnomad4 NFE AF: 0.0290

Gnomad4 OTH AF: 0.0378

Alfa AF: 0.0232 Hom.: 9

Bravo AF: 0.0260

Asia WGS AF: 0.124 AC: 432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.9
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490125; hg19: chr2-49124198;