Genetic Variant LINC03007:n.253-17453A>C (chr7-25679184-T-G) – 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 ENST00000456777.7(LINC03007):n.253-17453A>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: 32)

Consequence

LINC03007
ENST00000456777.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.54

Variant links:

Genes affected

LINC03007 (HGNC:56132): (long intergenic non-protein coding RNA 3007)

LINC03007 links:

ENSG00000286725 (HGNC:):

ENSG00000286725 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=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC03007	NR_157808.1 link	n.368-17453A>C	intron_variant	Intron 1 of 4
LINC03007	NR_157809.1 link	n.93-17453A>C	intron_variant	Intron 1 of 4
LINC03007	NR_157810.1 link	n.93-17453A>C	intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC03007	ENST00000456777.7 link	n.253-17453A>C	intron_variant	Intron 1 of 3	3
LINC03007	ENST00000659634.1 link	n.248-17453A>C	intron_variant	Intron 1 of 4
LINC03007	ENST00000671106.2 link	n.200-17453A>C	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.59

(source)

DANN

Benign

0.47

PhyloP100

-1.5

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

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over