rs7979870

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr12-126144376-T-A
• chr12-126144376-T-C
• chr12-126144376-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000643016.1(LINC02359):​n.495-10820T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

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>A		intron	N/A
	LINC02359	NR_186739.1		n.614-10820T>A		intron	N/A
	LINC02359	NR_186740.1		n.539-10820T>A		intron	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.73
DANN	Benign	0.27
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;