2-58655283-T-G

Variant names:

• chr2-58655283-T-G
• rs1159609
• ENST00000422723.5:n.264-1367T>G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000427421.5(LINC01122):​n.186-1367T>G variant causes a intron change. The variant allele was found at a frequency of 0.477 in 151,810 control chromosomes in the GnomAD database, including 17,493 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 0.48 (17493 hom., cov: 32)
• Consequence: LINC01122 ENST00000427421.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.87

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01122	NR_033873.1	n.186-1367T>G		intron_variant	Intron 1 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01122	ENST00000422723.5	n.264-1367T>G		intron_variant	Intron 2 of 5	3
LINC01122	ENST00000422793.3	n.122-1367T>G		intron_variant	Intron 2 of 6	5
LINC01122	ENST00000427421.5	n.186-1367T>G		intron_variant	Intron 1 of 13	2

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72387 AN: 151692 Hom.: 17476 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.477 AC: 72447 AN: 151810 Hom.: 17493 Cov.: 32 AF XY: 0.483 AC XY: 35808 AN XY: 74160

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.444

Alfa AF: 0.320 Hom.: 782

Bravo AF: 0.481

Asia WGS AF: 0.464 AC: 1614 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	20
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1159609; hg19: chr2-58882418;