rs10490109

Variant names:

• chr2-59161556-A-G
• rs10490109
• ENST00000422723.6:n.1150+25330A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000422723.6(LINC01122):​n.1150+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: LINC01122 ENST00000422723.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 3 publications found

Genes affected

LINC01122 (HGNC:49267): (long intergenic non-protein coding RNA 1122)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422723.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01122	ENST00000422723.6	TSL:3	n.1150+25330A>G		intron	N/A
	LINC01122	ENST00000650010.2		n.2172+25330A>G		intron	N/A
	LINC01122	ENST00000715766.1		n.1021+25330A>G		intron	N/A

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

African (AFR) AF: 0.389 AC: 16105 AN: 41448

American (AMR) AF: 0.302 AC: 4620 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1247 AN: 3468

East Asian (EAS) AF: 0.330 AC: 1704 AN: 5162

South Asian (SAS) AF: 0.365 AC: 1763 AN: 4824

European-Finnish (FIN) AF: 0.323 AC: 3408 AN: 10560

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 25009 AN: 67984

Other (OTH) AF: 0.369 AC: 780 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.20
DANN	Benign	0.45
PhyloP100		-1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10490109;

hg19: chr2-59388691;