ENST00000422723.6:n.884-17000G>A

Variant names:

• chr2-58997330-G-A
• rs1024766
• ENST00000422723.6:n.884-17000G>A

Variant summary

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

The ENST00000422723.6(LINC01122):​n.884-17000G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,924 control chromosomes in the GnomAD database, including 21,928 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 0.52 (21928 hom., cov: 32)
• Consequence: LINC01122 ENST00000422723.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510
• Publications: 4 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01122	NR_033873.1	n.834-6619G>A		intron_variant	Intron 6 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01122	ENST00000422723.6	n.884-17000G>A		intron_variant	Intron 6 of 10	3
LINC01122	ENST00000427421.5	n.834-6619G>A		intron_variant	Intron 6 of 13	2
LINC01122	ENST00000449448.6	n.639-6619G>A		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78516 AN: 151806 Hom.: 21887 Cov.: 32

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.517 AC: 78609 AN: 151924 Hom.: 21928 Cov.: 32 AF XY: 0.511 AC XY: 37918 AN XY: 74262

African (AFR) AF: 0.742 AC: 30733 AN: 41444

American (AMR) AF: 0.380 AC: 5799 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1743 AN: 3462

East Asian (EAS) AF: 0.310 AC: 1599 AN: 5162

South Asian (SAS) AF: 0.547 AC: 2632 AN: 4812

European-Finnish (FIN) AF: 0.392 AC: 4137 AN: 10560

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.448 AC: 30431 AN: 67910

Other (OTH) AF: 0.477 AC: 1005 AN: 2108

Alfa AF: 0.474 Hom.: 14000

Bravo AF: 0.523

Asia WGS AF: 0.451 AC: 1571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.36
PhyloP100		0.051

Splicing

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

Other links and lift over

dbSNP: rs1024766; hg19: chr2-59224465;