2-58510765-C-T

Variant names:

• chr2-58510765-C-T
• rs13387871
• ENST00000422723.6:n.263+82301C>T

Variant summary

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

The ENST00000422723.6(LINC01122):​n.263+82301C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 151,662 control chromosomes in the GnomAD database, including 6,453 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 0.27 (6453 hom., cov: 32)
• Consequence: LINC01122 ENST00000422723.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.434 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01122	ENST00000422723.6	TSL:3	n.263+82301C>T		intron	N/A
	LINC01122	ENST00000422793.4	TSL:5	n.134+48920C>T		intron	N/A
	LINC01122	ENST00000429095.6	TSL:4	n.195+48920C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40705 AN: 151542 Hom.: 6422 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.269 AC: 40784 AN: 151662 Hom.: 6453 Cov.: 32 AF XY: 0.268 AC XY: 19890 AN XY: 74082

African (AFR) AF: 0.439 AC: 18164 AN: 41340

American (AMR) AF: 0.202 AC: 3089 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 797 AN: 3466

East Asian (EAS) AF: 0.332 AC: 1705 AN: 5134

South Asian (SAS) AF: 0.328 AC: 1576 AN: 4808

European-Finnish (FIN) AF: 0.159 AC: 1669 AN: 10492

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13080 AN: 67848

Other (OTH) AF: 0.249 AC: 526 AN: 2110

Alfa AF: 0.198 Hom.: 1817

Bravo AF: 0.277

Asia WGS AF: 0.305 AC: 1058 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.37
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs13387871; hg19: chr2-58737900;