Genetic Variant ENST00000577798.6:n.374-15231G>A (chr17-13805544-C-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 ENST00000577798.6(COX10-DT):n.374-15231G>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
ENST00000577798.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.632

Publications

5 publications found

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 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=-0.87).

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.:

Alfa

AF:

0.00

Hom.:

137

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

(source)

DANN

Benign

0.75

PhyloP100

0.63

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