rs17269126

Variant names:

• chr2-58605272-A-G
• rs17269126
• ENST00000422723.6:n.264-51378A>G

Variant summary

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

The ENST00000422723.6(LINC01122):​n.264-51378A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0966 in 152,106 control chromosomes in the GnomAD database, including 861 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 0.097 (861 hom., cov: 31)
• Consequence: LINC01122 ENST00000422723.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 6 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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01122	NR_033873.1	n.186-51378A>G		intron_variant	Intron 1 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01122	ENST00000422723.6	n.264-51378A>G		intron_variant	Intron 2 of 10	3
LINC01122	ENST00000422793.4	n.135-51378A>G		intron_variant	Intron 2 of 6	5
LINC01122	ENST00000427421.5	n.186-51378A>G		intron_variant	Intron 1 of 13	2

Frequencies

GnomAD3 genomes AF: 0.0968 AC: 14705 AN: 151988 Hom.: 862 Cov.: 31

Gnomad AFR AF: 0.0225

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.0966 AC: 14690 AN: 152106 Hom.: 861 Cov.: 31 AF XY: 0.0979 AC XY: 7280 AN XY: 74342

African (AFR) AF: 0.0224 AC: 932 AN: 41518

American (AMR) AF: 0.105 AC: 1607 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 351 AN: 3470

East Asian (EAS) AF: 0.127 AC: 655 AN: 5168

South Asian (SAS) AF: 0.187 AC: 901 AN: 4816

European-Finnish (FIN) AF: 0.122 AC: 1288 AN: 10562

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8641 AN: 67978

Other (OTH) AF: 0.0962 AC: 203 AN: 2110

Alfa AF: 0.118 Hom.: 1953

Bravo AF: 0.0907

Asia WGS AF: 0.130 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.45
DANN	Benign	0.72
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs17269126; hg19: chr2-58832407;