12-126144376-T-C

Variant names:

• chr12-126144376-T-C
• rs7979870
• ENST00000643016.1:n.495-10820T>C

Variant summary

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

The ENST00000643016.1(LINC02359):​n.495-10820T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 152,080 control chromosomes in the GnomAD database, including 19,870 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 0.50 (19870 hom., cov: 33)
• Consequence: LINC02359 ENST00000643016.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35
• Publications: 1 publications found

Genes affected

LINC02359 (HGNC:53280): (long intergenic non-protein coding RNA 2359)

ENSG00000286386 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000643016.1. 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
	LINC02359	NR_186738.1		n.265-10820T>C		intron	N/A
	LINC02359	NR_186739.1		n.614-10820T>C		intron	N/A
	LINC02359	NR_186740.1		n.539-10820T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02359	ENST00000643016.1		n.495-10820T>C		intron	N/A
	LINC02359	ENST00000653935.1		n.218-10820T>C		intron	N/A
	LINC02359	ENST00000654753.1		n.608-10820T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76129 AN: 151962 Hom.: 19831 Cov.: 33

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.501 AC: 76228 AN: 152080 Hom.: 19870 Cov.: 33 AF XY: 0.501 AC XY: 37253 AN XY: 74330

African (AFR) AF: 0.586 AC: 24331 AN: 41486

American (AMR) AF: 0.484 AC: 7406 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1302 AN: 3472

East Asian (EAS) AF: 0.808 AC: 4169 AN: 5162

South Asian (SAS) AF: 0.526 AC: 2531 AN: 4816

European-Finnish (FIN) AF: 0.431 AC: 4554 AN: 10558

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30335 AN: 67980

Other (OTH) AF: 0.484 AC: 1021 AN: 2110

Alfa AF: 0.476 Hom.: 2294

Bravo AF: 0.507

Asia WGS AF: 0.655 AC: 2277 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	0.86
DANN	Benign	0.28
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs7979870; hg19: chr12-126628922;