Variant 17-14069166-C-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+106G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0516 in 191,130 control chromosomes in the GnomAD database, including 322 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.054 ( 288 hom., cov: 32)

Exomes 𝑓: 0.042 ( 34 hom. )

Consequence

COX10-DT
ENST00000449363.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.439

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=-0.9).

BP6

Variant 17-14069166-C-T is Benign according to our data. Variant chr17-14069166-C-T is described in ClinVar as [Benign]. Clinvar id is 1273311.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.073 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+106G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
COX10-DT	ENST00000449363.2 linkuse as main transcript	n.207+106G>A	intron_variant	2
COX10-DT	ENST00000582752.7 linkuse as main transcript	n.212+106G>A	intron_variant	3
COX10-DT	ENST00000602539.3 linkuse as main transcript	n.207+106G>A	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.0541

AC:

8231

AN:

152150

Hom.:

288

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0118

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.0434

Gnomad ASJ

AF:

0.0539

Gnomad EAS

AF:

0.0285

Gnomad SAS

AF:

0.0364

Gnomad FIN

AF:

0.128

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0747

Gnomad OTH

AF:

0.0545

GnomAD4 exome

AF:

0.0420

AC:

1633

AN:

38862

Hom.:

AF XY:

0.0391

AC XY:

793

AN XY:

20298

show subpopulations

Gnomad4 AFR exome

AF:

0.00514

Gnomad4 AMR exome

AF:

0.0215

Gnomad4 ASJ exome

AF:

0.0379

Gnomad4 EAS exome

AF:

0.0170

Gnomad4 SAS exome

AF:

0.0226

Gnomad4 FIN exome

AF:

0.0874

Gnomad4 NFE exome

AF:

0.0498

Gnomad4 OTH exome

AF:

0.0443

GnomAD4 genome

AF:

0.0540

AC:

8229

AN:

152268

Hom.:

288

Cov.:

AF XY:

0.0556

AC XY:

4142

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.0117

Gnomad4 AMR

AF:

0.0433

Gnomad4 ASJ

AF:

0.0539

Gnomad4 EAS

AF:

0.0283

Gnomad4 SAS

AF:

0.0362

Gnomad4 FIN

AF:

0.128

Gnomad4 NFE

AF:

0.0747

Gnomad4 OTH

AF:

0.0540

Alfa

AF:

0.0661

Hom.:

Bravo

AF:

0.0448

Asia WGS

AF:

0.0310

AC:

106

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 28, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.4

DANN

Benign

0.90

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