ENST00000681662.1:n.129C>T

Variant names:

• chr4-111959712-C-T
• rs877936
• ENST00000681662.1:n.129C>T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000681662.1(ENSG00000288685):​n.129C>T 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: ENSG00000288685 ENST00000681662.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317

Genes affected

ENSG00000288685 (HGNC:):

LINC02945 (HGNC:55960): (long intergenic non-protein coding RNA 2945)

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=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02945	NR_186680.1	n.98+112853G>A		intron_variant	Intron 1 of 2
LINC02945	NR_186681.1	n.184+60702G>A		intron_variant	Intron 2 of 3
LINC02945	NR_186682.1	n.83-130662G>A		intron_variant	Intron 1 of 2
LINC02945	NR_186683.1	n.62+112889G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288685	ENST00000681662.1	n.129C>T		non_coding_transcript_exon_variant	Exon 1 of 3
LINC02945	ENST00000511219.1	n.134+112853G>A		intron_variant	Intron 1 of 2	3
LINC02945	ENST00000679735.1	n.187+60702G>A		intron_variant	Intron 2 of 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	-0.91
CADD	Benign	1.3
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs877936; hg19: chr4-112880868;