chr2-242106609-C-A

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -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

Genes affected

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

ENSG00000291147 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01881	NR_130699.1	n.311-8030C>A		intron_variant	Intron 2 of 7
LINC01881	NR_130700.1	n.310+11582C>A		intron_variant	Intron 2 of 5
LINC01881	NR_130701.1	n.311-8030C>A		intron_variant	Intron 2 of 7
LINC01881	NR_130702.1	n.311-8030C>A		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01881	ENST00000416103.2	n.135-8030C>A		intron_variant	Intron 1 of 4	6
ENSG00000291147	ENST00000431796.5	n.251-8030C>A		intron_variant	Intron 2 of 4	4
ENSG00000291147	ENST00000444990.7	n.306-8030C>A		intron_variant	Intron 2 of 3	3

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	-0.70
CADD	Benign	3.0
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12478296; hg19: chr2-243048760;