2-58867055-G-A

Variant names:

• chr2-58867055-G-A
• rs6719683
• ENST00000422723.6:n.502+16449G>A

Variant summary

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

The ENST00000422723.6(LINC01122):​n.502+16449G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 151,828 control chromosomes in the GnomAD database, including 9,478 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 0.34 (9478 hom., cov: 32)
• Consequence: LINC01122 ENST00000422723.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.496 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.424+16449G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01122	ENST00000422723.6	TSL:3	n.502+16449G>A		intron	N/A
	LINC01122	ENST00000422793.4	TSL:5	n.373+16449G>A		intron	N/A
	LINC01122	ENST00000427421.5	TSL:2	n.424+16449G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51142 AN: 151710 Hom.: 9462 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.337 AC: 51209 AN: 151828 Hom.: 9478 Cov.: 32 AF XY: 0.337 AC XY: 25026 AN XY: 74194

African (AFR) AF: 0.502 AC: 20775 AN: 41378

American (AMR) AF: 0.289 AC: 4411 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 993 AN: 3462

East Asian (EAS) AF: 0.389 AC: 1983 AN: 5096

South Asian (SAS) AF: 0.306 AC: 1475 AN: 4816

European-Finnish (FIN) AF: 0.273 AC: 2882 AN: 10570

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17645 AN: 67930

Other (OTH) AF: 0.327 AC: 689 AN: 2110

Alfa AF: 0.286 Hom.: 21278

Bravo AF: 0.346

Asia WGS AF: 0.373 AC: 1298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.66
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs6719683; hg19: chr2-59094190;