ENST00000422723.5:n.326-11757G>A

Variant names:

• chr2-58838673-G-A
• rs7593324
• ENST00000422723.6:n.326-11757G>A

Variant summary

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

The ENST00000422723.6(LINC01122):​n.326-11757G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 151,890 control chromosomes in the GnomAD database, including 1,652 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 0.14 (1652 hom., cov: 32)
• Consequence: LINC01122 ENST00000422723.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352
• 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 = 0.197 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01122	NR_033873.1		n.248-11757G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01122	ENST00000422723.6	TSL:3	n.326-11757G>A		intron	N/A
	LINC01122	ENST00000422793.4	TSL:5	n.197-11757G>A		intron	N/A
	LINC01122	ENST00000427421.5	TSL:2	n.248-11757G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21332 AN: 151772 Hom.: 1649 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.0921

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.141 AC: 21351 AN: 151890 Hom.: 1652 Cov.: 32 AF XY: 0.141 AC XY: 10446 AN XY: 74256

African (AFR) AF: 0.201 AC: 8326 AN: 41444

American (AMR) AF: 0.112 AC: 1707 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 572 AN: 3466

East Asian (EAS) AF: 0.172 AC: 881 AN: 5132

South Asian (SAS) AF: 0.180 AC: 866 AN: 4820

European-Finnish (FIN) AF: 0.0921 AC: 976 AN: 10596

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7497 AN: 67890

Other (OTH) AF: 0.145 AC: 307 AN: 2112

Alfa AF: 0.125 Hom.: 4268

Bravo AF: 0.145

Asia WGS AF: 0.204 AC: 710 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	0.57
DANN	Benign	0.38
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs7593324; hg19: chr2-59065808;