Variant chr17-14069205-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000449363.2(COX10-DT):n.207+67G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0193 in 279,358 control chromosomes in the GnomAD database, including 119 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.027 ( 103 hom., cov: 32)

Exomes 𝑓: 0.010 ( 16 hom. )

Consequence

COX10-DT
ENST00000449363.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0290

Variant links:

Genes affected

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

COX10-DT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 17-14069205-C-T is Benign according to our data. Variant chr17-14069205-C-T is described in ClinVar as [Benign]. Clinvar id is 673119.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COX10-DT	NR_049718.1 link	n.187+67G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
COX10-DT	ENST00000449363.2 link	n.207+67G>A	intron_variant	2
COX10-DT	ENST00000582752.7 link	n.212+67G>A	intron_variant	3
COX10-DT	ENST00000602539.3 link	n.207+67G>A	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.0269

AC:

4095

AN:

152190

Hom.:

105

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0732

Gnomad AMI

AF:

0.0560

Gnomad AMR

AF:

0.0175

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0118

Gnomad FIN

AF:

0.00254

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.00854

Gnomad OTH

AF:

0.0249

GnomAD4 exome

AF:

0.0101

AC:

1289

AN:

127050

Hom.:

AF XY:

0.00960

AC XY:

645

AN XY:

67170

show subpopulations

Gnomad4 AFR exome

AF:

0.0689

Gnomad4 AMR exome

AF:

0.00963

Gnomad4 ASJ exome

AF:

0.000314

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00883

Gnomad4 FIN exome

AF:

0.00154

Gnomad4 NFE exome

AF:

0.00896

Gnomad4 OTH exome

AF:

0.0121

GnomAD4 genome

AF:

0.0269

AC:

4090

AN:

152308

Hom.:

103

Cov.:

AF XY:

0.0264

AC XY:

1963

AN XY:

74476

show subpopulations

Gnomad4 AFR

AF:

0.0729

Gnomad4 AMR

AF:

0.0175

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0114

Gnomad4 FIN

AF:

0.00254

Gnomad4 NFE

AF:

0.00854

Gnomad4 OTH

AF:

0.0246

Alfa

AF:

0.0206

Hom.:

Bravo

AF:

0.0296

Asia WGS

AF:

0.00635

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 14, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

4.9

DANN

Benign

0.84

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over