rs12478296

Variant names:

• chr2-242106609-C-A
• rs12478296
• ENST00000416103.2:n.135-8030C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-242106609-C-A
• chr2-242106609-C-T

Variant summary

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

The ENST00000614114.4(ENSG00000291147):​n.248-8030C>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: 32)
• Consequence: ENSG00000291147 ENST00000614114.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.289
• Publications: 11 publications found

Genes affected

LINC01881 (HGNC:52700): (long intergenic non-protein coding RNA 1881)

ENSG00000291147 (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=-0.7).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000614114.4. 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
	LINC01881	NR_130699.1		n.311-8030C>A		intron	N/A
	LINC01881	NR_130700.1		n.310+11582C>A		intron	N/A
	LINC01881	NR_130701.1		n.311-8030C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01881	ENST00000416103.2	TSL:6	n.135-8030C>A		intron	N/A
	ENSG00000291147	ENST00000431796.6	TSL:4	n.260-8030C>A		intron	N/A
	ENSG00000291147	ENST00000433444.2	TSL:3	n.285-8030C>A		intron	N/A

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

Alfa AF: 0.00 Hom.: 3344

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	3.0
DANN	Benign	0.88
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs12478296; hg19: chr2-243048760;