ENST00000422723.6:n.326-4596C>T

Variant names:

• chr2-58845834-C-T
• rs17552189
• ENST00000422723.6:n.326-4596C>T

Variant summary

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

The ENST00000422723.6(LINC01122):​n.326-4596C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,782 control chromosomes in the GnomAD database, including 7,254 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 0.29 (7254 hom., cov: 32)
• Consequence: LINC01122 ENST00000422723.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188
• Publications: 11 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01122	NR_033873.1	n.248-4596C>T		intron_variant	Intron 2 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01122	ENST00000422723.6	n.326-4596C>T		intron_variant	Intron 3 of 10	3
LINC01122	ENST00000422793.4	n.197-4596C>T		intron_variant	Intron 3 of 6	5
LINC01122	ENST00000427421.5	n.248-4596C>T		intron_variant	Intron 2 of 13	2

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44505 AN: 151664 Hom.: 7257 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.293 AC: 44511 AN: 151782 Hom.: 7254 Cov.: 32 AF XY: 0.288 AC XY: 21360 AN XY: 74164

African (AFR) AF: 0.174 AC: 7210 AN: 41440

American (AMR) AF: 0.254 AC: 3871 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1008 AN: 3466

East Asian (EAS) AF: 0.140 AC: 721 AN: 5138

South Asian (SAS) AF: 0.202 AC: 971 AN: 4804

European-Finnish (FIN) AF: 0.353 AC: 3724 AN: 10550

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.384 AC: 26022 AN: 67852

Other (OTH) AF: 0.297 AC: 627 AN: 2110

Alfa AF: 0.351 Hom.: 30925

Bravo AF: 0.282

Asia WGS AF: 0.162 AC: 564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.24
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs17552189; hg19: chr2-59072969;