Genetic Variant COX10-DT:n.374-15231G>A (chr17-13805544-C-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000602539.3(COX10-DT):n.870-28195G>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: 29)

Consequence

COX10-DT
ENST00000602539.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.632

Variant links:

Genes affected

COX10-DT (HGNC:38873): (COX10 divergent transcript)

COX10-DT links:

LOC100506974 (HGNC:):

LOC100506974 links:

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ACMG classification

Classification made for transcript

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=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC100506974	XR_001752794.1 link	n.388-14469G>A	intron_variant	Intron 2 of 2
LOC100506974	XR_001752796.1 link	n.388-14511G>A	intron_variant	Intron 2 of 2
LOC100506974	XR_001752797.1 link	n.321-14469G>A	intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
COX10-DT	ENST00000577798.6 link	n.374-15231G>A	intron_variant	Intron 3 of 4	3
COX10-DT	ENST00000582752.7 link	n.810-48815G>A	intron_variant	Intron 4 of 4	3
COX10-DT	ENST00000602539.3 link	n.870-28195G>A	intron_variant	Intron 4 of 4	2

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

Bravo

AF:

0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.2

DANN

Benign

0.75

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over