rs10490109

Variant names:

• chr2-59161556-A-G
• rs10490109
• ENST00000650010.1:n.1424+25330A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-59161556-A-G
• chr2-59161556-A-T

Variant summary

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

The ENST00000650010.1(ENSG00000285673):​n.1424+25330A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 152,036 control chromosomes in the GnomAD database, including 10,056 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 0.36 (10056 hom., cov: 32)
• Consequence: ENSG00000285673 ENST00000650010.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

ENSG00000285673 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 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
ENSG00000285673	ENST00000650010.1	n.1424+25330A>G		intron_variant	Intron 7 of 8

Frequencies

GnomAD3 genomes AF: 0.362 AC: 55061 AN: 151916 Hom.: 10056 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.362 AC: 55082 AN: 152036 Hom.: 10056 Cov.: 32 AF XY: 0.360 AC XY: 26747 AN XY: 74324

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.369

Alfa AF: 0.352 Hom.: 1304

Bravo AF: 0.361

Asia WGS AF: 0.383 AC: 1328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.20
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490109; hg19: chr2-59388691;