Genetic Variant LINC00882:n.628+22969C>A (chr3-106897997-G-T) – 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 ENST00000484698.5(LINC00882):n.628+22969C>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: 31)

Consequence

LINC00882
ENST00000484698.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.899

Publications

1 publications found

Variant links:

Genes affected

LINC00882 (HGNC:48568): (long intergenic non-protein coding RNA 882)

LINC00882 links:

MTATP6P22 (HGNC:52178): (MT-ATP6 pseudogene 22)

MTATP6P22 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=-0.68).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000484698.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
LINC00882	ENST00000484698.5	TSL:1	n.628+22969C>A	intron	N/A
MTATP6P22	ENST00000507369.1	TSL:6	n.272C>A	non_coding_transcript_exon	Exon 1 of 1
LINC00882	ENST00000655451.1		n.729+15045C>A	intron	N/A

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

0.11

(source)

DANN

Benign

0.31

PhyloP100

0.90

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over