chr2-58921975-T-A

Variant names:

• chr2-58921975-T-A
• rs6545708
• ENST00000422723.6:n.503-2570T>A

Variant summary

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

The ENST00000427421.5(LINC01122):​n.453-2570T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,948 control chromosomes in the GnomAD database, including 18,746 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 0.49 (18746 hom., cov: 31)
• Consequence: LINC01122 ENST00000427421.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323
• Publications: 0 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 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.453-2570T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01122	ENST00000422723.6	TSL:3	n.503-2570T>A		intron	N/A
	LINC01122	ENST00000422793.4	TSL:5	n.374-2570T>A		intron	N/A
	LINC01122	ENST00000427421.5	TSL:2	n.453-2570T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74651 AN: 151830 Hom.: 18730 Cov.: 31

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.492 AC: 74707 AN: 151948 Hom.: 18746 Cov.: 31 AF XY: 0.492 AC XY: 36560 AN XY: 74264

African (AFR) AF: 0.547 AC: 22645 AN: 41418

American (AMR) AF: 0.484 AC: 7388 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1621 AN: 3468

East Asian (EAS) AF: 0.716 AC: 3685 AN: 5146

South Asian (SAS) AF: 0.409 AC: 1972 AN: 4822

European-Finnish (FIN) AF: 0.461 AC: 4865 AN: 10564

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30931 AN: 67946

Other (OTH) AF: 0.480 AC: 1010 AN: 2106

Alfa AF: 0.312 Hom.: 735

Bravo AF: 0.499

Asia WGS AF: 0.538 AC: 1872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.9
DANN	Benign	0.45
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs6545708; hg19: chr2-59149110;