Genetic Variant LINC02668:n.887+2979C>G (chr10-3253481-G-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

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

The ENST00000417149.2(LINC02668):n.887+2979C>G 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

LINC02668
ENST00000417149.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.657

Publications

2 publications found

Variant links:

Genes affected

LINC02668 (HGNC:54154): (long intergenic non-protein coding RNA 2668)

LINC02668 links:

LOC105376353 (HGNC:):

LOC105376353 links:

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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=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02668	NR_187502.1 link	n.474+2979C>G	intron_variant	Intron 2 of 3
LINC02668	NR_187504.1 link	n.474+2979C>G	intron_variant	Intron 2 of 2
LINC02668	NR_187506.1 link	n.474+2979C>G	intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02668	ENST00000417149.2 link	n.887+2979C>G	intron_variant	Intron 2 of 6	3
LINC02668	ENST00000655354.1 link	n.539+2979C>G	intron_variant	Intron 2 of 4
LINC02668	ENST00000665182.1 link	n.539+2979C>G	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

7472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.64

(source)

DANN

Benign

0.34

PhyloP100

-0.66

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over