rs12587874

Variant names:

• chr14-28984835-A-C
• rs12587874
• ENST00000551227.1:n.108-1565A>C

Your query was ambiguous. Multiple possible variants found:

• chr14-28984835-A-C
• chr14-28984835-A-G

Variant summary

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

The ENST00000551227.1(LINC02327):​n.108-1565A>C 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: 32)
• Consequence: LINC02327 ENST00000551227.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.63
• Publications: 1 publications found

Genes affected

LINC02327 (HGNC:53247): (long intergenic non-protein coding RNA 2327)

LINC02326 (HGNC:53246): (long intergenic non-protein coding RNA 2326)

ENSG00000257522 (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=-0.51).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02326	NR_184205.1	n.338-5817T>G		intron_variant	Intron 4 of 6
LINC02326	NR_184206.1	n.237-5817T>G		intron_variant	Intron 2 of 4
LOC107984685	XR_007064101.1	n.202-1565A>C		intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02327	ENST00000551227.1	n.108-1565A>C		intron_variant	Intron 1 of 5	5
LINC02326	ENST00000552028.2	n.462-5817T>G		intron_variant	Intron 5 of 7	3
LINC02326	ENST00000650159.1	n.292+44605T>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	13
DANN	Benign	0.86
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs12587874; hg19: chr14-29454041;