chr12-31886553-C-T

Variant names:

• chr12-31886553-C-T
• rs1797779
• ENST00000752261.1:n.711G>A

Variant summary

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

The ENST00000752261.1(LINC02422):​n.711G>A variant causes a non coding transcript exon 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 ENST00000752261.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752261.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02422	NR_135029.1		n.37+614G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02422	ENST00000752261.1		n.711G>A		non_coding_transcript_exon	Exon 1 of 1
	LINC02422	ENST00000535163.2	TSL:3	n.52+614G>A		intron	N/A
	LINC02422	ENST00000662662.1		n.369-8660G>A		intron	N/A

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

African (AFR) AF: 0.805 AC: 33418 AN: 41506

American (AMR) AF: 0.910 AC: 13904 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.903 AC: 3136 AN: 3472

East Asian (EAS) AF: 0.993 AC: 5146 AN: 5182

South Asian (SAS) AF: 0.891 AC: 4297 AN: 4820

European-Finnish (FIN) AF: 0.939 AC: 9967 AN: 10612

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.873 AC: 59407 AN: 68022

Other (OTH) AF: 0.883 AC: 1867 AN: 2114

Alfa AF: 0.871 Hom.: 29492

Bravo AF: 0.865

Asia WGS AF: 0.931 AC: 3237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.70
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1797779; hg19: chr12-32039487;