rs10211390

Variant names:

• chr2-59093319-C-G
• rs10211390
• ENST00000422723.6:n.1043-42800C>G

Variant summary

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

The ENST00000422723.6(LINC01122):​n.1043-42800C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 152,064 control chromosomes in the GnomAD database, including 16,953 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 0.45 (16953 hom., cov: 32)
• Consequence: LINC01122 ENST00000422723.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• 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 = 0.649 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.1043-42800C>G		intron	N/A
	LINC01122	ENST00000650010.2		n.1992-14438C>G		intron	N/A
	LINC01122	ENST00000715766.1		n.914-42800C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68723 AN: 151946 Hom.: 16928 Cov.: 32

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.452 AC: 68805 AN: 152064 Hom.: 16953 Cov.: 32 AF XY: 0.451 AC XY: 33504 AN XY: 74326

African (AFR) AF: 0.656 AC: 27203 AN: 41484

American (AMR) AF: 0.436 AC: 6659 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1209 AN: 3472

East Asian (EAS) AF: 0.350 AC: 1806 AN: 5158

South Asian (SAS) AF: 0.392 AC: 1891 AN: 4820

European-Finnish (FIN) AF: 0.401 AC: 4234 AN: 10564

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24531 AN: 67968

Other (OTH) AF: 0.408 AC: 862 AN: 2112

Alfa AF: 0.412 Hom.: 1893

Bravo AF: 0.465

Asia WGS AF: 0.379 AC: 1320 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	0.075
DANN	Benign	0.41
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10211390; hg19: chr2-59320454;