rs17269126

Positions:

• chr2-58605272-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_033873.1(LINC01122):​n.186-51378A>G variant causes a intron, non coding transcript 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 NR_033873.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01122	NR_033873.1	n.186-51378A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01122	ENST00000452840.5	n.196-51378A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.0224

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.0962

Alfa AF: 0.121 Hom.: 1620

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17269126; hg19: chr2-58832407;