Variant chr17-14069201-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000449363.2(COX10-DT):n.207+71C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00905 in 276,566 control chromosomes in the GnomAD database, including 85 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0093 ( 53 hom., cov: 32)

Exomes 𝑓: 0.0087 ( 32 hom. )

Consequence

COX10-DT
ENST00000449363.2 intron

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.205

Variant links:

Genes affected

COX10-DT (HGNC:):

COX10-DT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 17-14069201-G-T is Benign according to our data. Variant chr17-14069201-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 1216738.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COX10-DT	NR_049718.1 linkuse as main transcript	n.187+71C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
COX10-DT	ENST00000449363.2 linkuse as main transcript	n.207+71C>A	intron_variant	2
COX10-DT	ENST00000582752.7 linkuse as main transcript	n.212+71C>A	intron_variant	3
COX10-DT	ENST00000602539.3 linkuse as main transcript	n.207+71C>A	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.00927

AC:

1411

AN:

152182

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00166

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0418

Gnomad ASJ

AF:

0.00720

Gnomad EAS

AF:

0.0775

Gnomad SAS

AF:

0.00745

Gnomad FIN

AF:

0.0158

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000794

Gnomad OTH

AF:

0.00909

GnomAD4 exome

AF:

0.00869

AC:

1080

AN:

124266

Hom.:

AF XY:

0.00889

AC XY:

585

AN XY:

65816

show subpopulations

Gnomad4 AFR exome

AF:

0.00121

Gnomad4 AMR exome

AF:

0.0561

Gnomad4 ASJ exome

AF:

0.00480

Gnomad4 EAS exome

AF:

0.0883

Gnomad4 SAS exome

AF:

0.00449

Gnomad4 FIN exome

AF:

0.0127

Gnomad4 NFE exome

AF:

0.000419

Gnomad4 OTH exome

AF:

0.00694

GnomAD4 genome

AF:

0.00934

AC:

1422

AN:

152300

Hom.:

Cov.:

AF XY:

0.0111

AC XY:

828

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.00166

Gnomad4 AMR

AF:

0.0419

Gnomad4 ASJ

AF:

0.00720

Gnomad4 EAS

AF:

0.0781

Gnomad4 SAS

AF:

0.00745

Gnomad4 FIN

AF:

0.0158

Gnomad4 NFE

AF:

0.000794

Gnomad4 OTH

AF:

0.0123

Alfa

AF:

0.00609

Hom.:

Bravo

AF:

0.0127

Asia WGS

AF:

0.0540

AC:

186

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 15, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.57

DANN

Benign

0.59

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