rs1797779

Positions:

• chr12-31886553-C-T

Variant summary

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

The NR_135029.1(LINC02422):​n.37+614G>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 0.868 in 152,216 control chromosomes in the GnomAD database, including 57,612 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 0.87 (57612 hom., cov: 33)
• Consequence: LINC02422 NR_135029.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

Genes affected

LINC02422 (HGNC:53352): (long intergenic non-protein coding RNA 2422)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02422	NR_135029.1	n.37+614G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02422	ENST00000662662.1	n.369-8660G>A		intron_variant, non_coding_transcript_variant
LINC02422	ENST00000535163.1	n.37+614G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.868 AC: 132089 AN: 152098 Hom.: 57577 Cov.: 33

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.903

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.939

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.882

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

GnomAD4 genome AF: 0.868 AC: 132178 AN: 152216 Hom.: 57612 Cov.: 33 AF XY: 0.873 AC XY: 64991 AN XY: 74416

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.910

Gnomad4 ASJ AF: 0.903

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.891

Gnomad4 FIN AF: 0.939

Gnomad4 NFE AF: 0.873

Gnomad4 OTH AF: 0.883

Alfa AF: 0.872 Hom.: 26317

Bravo AF: 0.865

Asia WGS AF: 0.931 AC: 3237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1797779; hg19: chr12-32039487;