3-141689849-A-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000474979.4(ENSG00000293386):​n.874-583A>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: 30)

Consequence

ENSG00000293386
ENST00000474979.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.622

Publications

3 publications found
Variant links:
Genes affected
ENSG00000293386 (HGNC:54091): (long intergenic non-protein coding RNA 2618)

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ACMG classification

Classification was made for transcript

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=-0.91).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LRRC78PNR_136190.1 linkn.663-583A>C intron_variant Intron 5 of 7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000293386ENST00000474979.4 linkn.874-583A>C intron_variant Intron 6 of 9 5
LRRC78PENST00000637590.2 linkn.770-583A>C intron_variant Intron 5 of 8 6
ENSG00000293386ENST00000819704.1 linkn.746-583A>C intron_variant Intron 5 of 5

Frequencies

GnomAD3 genomes
Cov.:
30
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
30
Alfa
AF:
0.00
Hom.:
109395

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.42
DANN
Benign
0.41
PhyloP100
-0.62

Splicing

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

Publications

Other links and lift over

dbSNP: rs6440031; hg19: chr3-141408691; API