rs2192692

Variant names:

• chr2-58877389-G-A
• rs2192692
• ENST00000422723.6:n.502+26783G>A

Variant summary

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

The ENST00000427421.5(LINC01122):​n.424+26783G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 151,934 control chromosomes in the GnomAD database, including 32,039 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 0.63 (32039 hom., cov: 31)
• Consequence: LINC01122 ENST00000427421.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000427421.5. 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
	LINC01122	NR_033873.1		n.424+26783G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01122	ENST00000422723.6	TSL:3	n.502+26783G>A		intron	N/A
	LINC01122	ENST00000422793.4	TSL:5	n.373+26783G>A		intron	N/A
	LINC01122	ENST00000427421.5	TSL:2	n.424+26783G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96040 AN: 151816 Hom.: 32007 Cov.: 31

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.633 AC: 96129 AN: 151934 Hom.: 32039 Cov.: 31 AF XY: 0.630 AC XY: 46725 AN XY: 74222

African (AFR) AF: 0.843 AC: 34980 AN: 41498

American (AMR) AF: 0.512 AC: 7810 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2192 AN: 3470

East Asian (EAS) AF: 0.325 AC: 1669 AN: 5132

South Asian (SAS) AF: 0.558 AC: 2675 AN: 4798

European-Finnish (FIN) AF: 0.609 AC: 6421 AN: 10552

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38343 AN: 67932

Other (OTH) AF: 0.602 AC: 1267 AN: 2104

Alfa AF: 0.579 Hom.: 49312

Bravo AF: 0.635

Asia WGS AF: 0.475 AC: 1653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.76
DANN	Benign	0.53
PhyloP100		-0.053

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: rs2192692;

hg19: chr2-59104524;