rs2192692

chr2-58877389-G-A

Variant summary

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

The NR_033873.1(LINC01122):n.424+26783G>A 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 0.633 in 151,934 control chromosomes in the GnomAD database, including 32,039 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 0.63 (32039 hom., cov: 31)
• Consequence: LINC01122 NR_033873.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01122	NR_033873.1	n.424+26783G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01122	ENST00000452840.5	n.434+26783G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96040 AN: 151816 Hom.: 32007 Cov.: 31

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.633 AC: 96129 AN: 151934 Hom.: 32039 Cov.: 31 AF XY: 0.630 AC XY: 46725 AN XY: 74222

Gnomad4 AFR AF: 0.843

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.602

Alfa AF: 0.573 Hom.: 34908

Bravo AF: 0.635

Asia WGS AF: 0.475 AC: 1653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.76
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2192692; hg19: chr2-59104524;