12-126874646-T-G

Variant names:

• chr12-126874646-T-G
• rs7970012
• ENST00000507482.7:n.49A>C

Variant summary

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

The ENST00000507482.7(LINC02372):​n.49A>C variant causes a non coding transcript exon 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: 32)
• Consequence: LINC02372 ENST00000507482.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 6 publications found

Genes affected

LINC02372 (HGNC:53294): (long intergenic non-protein coding RNA 2372)

ENSG00000256286 (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=-0.95).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02372	NR_033970.1	n.45A>C		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105370061	XR_001749174.2	n.-158T>G		upstream_gene_variant
LOC105370061	XR_007063516.1	n.-158T>G		upstream_gene_variant
LOC105370061	XR_945511.3	n.-158T>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02372	ENST00000507482.7	n.49A>C		non_coding_transcript_exon_variant	Exon 1 of 3	1
LINC02372	ENST00000541348.2	n.26A>C		non_coding_transcript_exon_variant	Exon 1 of 3	3
LINC02372	ENST00000544727.3	n.71A>C		non_coding_transcript_exon_variant	Exon 1 of 3	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.0
DANN	Benign	0.36
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs7970012; hg19: chr12-127359192;