rs7592415

Variant names:

• chr2-58845381-A-G
• rs7592415
• ENST00000422723.6:n.326-5049A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000422723.6(LINC01122):​n.326-5049A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,918 control chromosomes in the GnomAD database, including 9,239 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 0.32 (9239 hom., cov: 32)
• Consequence: LINC01122 ENST00000422723.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.622
• Publications: 2 publications found

Genes affected

LINC01122 (HGNC:49267): (long intergenic non-protein coding RNA 1122)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01122	NR_033873.1	n.248-5049A>G		intron_variant	Intron 2 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01122	ENST00000422723.6	n.326-5049A>G		intron_variant	Intron 3 of 10	3
LINC01122	ENST00000422793.4	n.197-5049A>G		intron_variant	Intron 3 of 6	5
LINC01122	ENST00000427421.5	n.248-5049A>G		intron_variant	Intron 2 of 13	2

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49097 AN: 151800 Hom.: 9214 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.324 AC: 49169 AN: 151918 Hom.: 9239 Cov.: 32 AF XY: 0.323 AC XY: 24010 AN XY: 74238

African (AFR) AF: 0.532 AC: 22080 AN: 41476

American (AMR) AF: 0.227 AC: 3459 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 888 AN: 3470

East Asian (EAS) AF: 0.230 AC: 1181 AN: 5128

South Asian (SAS) AF: 0.305 AC: 1468 AN: 4812

European-Finnish (FIN) AF: 0.272 AC: 2883 AN: 10584

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16262 AN: 67892

Other (OTH) AF: 0.312 AC: 657 AN: 2106

Alfa AF: 0.266 Hom.: 18948

Bravo AF: 0.328

Asia WGS AF: 0.314 AC: 1092 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	6.8
DANN	Benign	0.56
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs7592415; hg19: chr2-59072516;