chr12-92990459-G-A

Variant names:

• chr12-92990459-G-A
• rs4760516
• ENST00000755877.1:n.105-228G>A

Variant summary

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

The ENST00000755877.1(LINC02413):​n.105-228G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 151,888 control chromosomes in the GnomAD database, including 30,939 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 (30939 hom., cov: 31)
• Consequence: LINC02413 ENST00000755877.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 2 publications found

Genes affected

LINC02413 (HGNC:53342): (long intergenic non-protein coding RNA 2413)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755877.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02413	ENST00000755877.1		n.105-228G>A		intron	N/A
	LINC02413	ENST00000755878.1		n.199-228G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96279 AN: 151770 Hom.: 30928 Cov.: 31

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.634 AC: 96317 AN: 151888 Hom.: 30939 Cov.: 31 AF XY: 0.637 AC XY: 47268 AN XY: 74198

African (AFR) AF: 0.534 AC: 22095 AN: 41412

American (AMR) AF: 0.685 AC: 10446 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2083 AN: 3468

East Asian (EAS) AF: 0.700 AC: 3612 AN: 5160

South Asian (SAS) AF: 0.689 AC: 3307 AN: 4802

European-Finnish (FIN) AF: 0.683 AC: 7202 AN: 10542

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.669 AC: 45480 AN: 67944

Other (OTH) AF: 0.622 AC: 1313 AN: 2110

Alfa AF: 0.654 Hom.: 51288

Bravo AF: 0.630

Asia WGS AF: 0.676 AC: 2348 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.7
DANN	Benign	0.31
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs4760516; hg19: chr12-93384235;