2-58820784-T-G

Variant names:

• chr2-58820784-T-G
• rs2160206
• ENST00000422723.6:n.326-29646T>G

Variant summary

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

The ENST00000422723.6(LINC01122):​n.326-29646T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 152,090 control chromosomes in the GnomAD database, including 41,656 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 0.74 (41656 hom., cov: 32)
• Consequence: LINC01122 ENST00000422723.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.819 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01122	NR_033873.1		n.248-29646T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01122	ENST00000422723.6	TSL:3	n.326-29646T>G		intron	N/A
	LINC01122	ENST00000422793.4	TSL:5	n.197-29646T>G		intron	N/A
	LINC01122	ENST00000427421.5	TSL:2	n.248-29646T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112143 AN: 151972 Hom.: 41610 Cov.: 32

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.738 AC: 112243 AN: 152090 Hom.: 41656 Cov.: 32 AF XY: 0.740 AC XY: 55008 AN XY: 74336

African (AFR) AF: 0.826 AC: 34296 AN: 41522

American (AMR) AF: 0.700 AC: 10697 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2220 AN: 3468

East Asian (EAS) AF: 0.775 AC: 4002 AN: 5162

South Asian (SAS) AF: 0.664 AC: 3196 AN: 4814

European-Finnish (FIN) AF: 0.782 AC: 8264 AN: 10570

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47303 AN: 67974

Other (OTH) AF: 0.721 AC: 1519 AN: 2108

Alfa AF: 0.706 Hom.: 159122

Bravo AF: 0.736

Asia WGS AF: 0.726 AC: 2524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.2
DANN	Benign	0.58
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs2160206; hg19: chr2-59047919;