Variant 20-18138018-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The ENST00000432901.4(PET117):c.63C>T(p.Ala21=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00467 in 1,498,000 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0040 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0047 ( 22 hom. )

Consequence

PET117
ENST00000432901.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.15

Variant links:

Genes affected

PET117 (HGNC:40045): (PET117 cytochrome c oxidase chaperone) Predicted to be involved in mitochondrial cytochrome c oxidase assembly. Located in mitochondrion. Implicated in cytochrome-c oxidase deficiency disease. [provided by Alliance of Genome Resources, Apr 2022]

PET117 links:

KAT14 (HGNC:15904): (lysine acetyltransferase 14) CSRP2 is a protein containing two LIM domains, which are double zinc finger motifs found in proteins of diverse function. CSRP2 and some related proteins are thought to act as protein adapters, bridging two or more proteins to form a larger protein complex. The protein encoded by this gene binds to one of the LIM domains of CSRP2 and contains an acetyltransferase domain. Although the encoded protein has been detected in the cytoplasm, it is predominantly a nuclear protein. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jun 2011]

KAT14 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BP6

Variant 20-18138018-C-T is Benign according to our data. Variant chr20-18138018-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2652219.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.15 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PET117	NM_001164811.2 linkuse as main transcript	c.63C>T	p.Ala21=	synonymous_variant	1/2	ENST00000432901.4	NP_001158283.1
KAT14	NM_001392073.1 linkuse as main transcript	c.-487C>T		5_prime_UTR_variant	1/11	ENST00000688188.1	NP_001379002.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PET117	ENST00000432901.4 linkuse as main transcript	c.63C>T	p.Ala21=	synonymous_variant	1/2	1	NM_001164811.2	ENSP00000397881	P1
KAT14	ENST00000688188.1 linkuse as main transcript	c.-487C>T		5_prime_UTR_variant	1/11		NM_001392073.1	ENSP00000508684	A1

Frequencies

GnomAD3 genomes

AF:

0.00397

AC:

604

AN:

151990

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000700

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00308

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.00868

Gnomad MID

AF:

0.0159

Gnomad NFE

AF:

0.00584

Gnomad OTH

AF:

0.0105

GnomAD3 exomes

AF:

0.00338

AC:

334

AN:

98744

Hom.:

AF XY:

0.00340

AC XY:

186

AN XY:

54666

show subpopulations

Gnomad AFR exome

AF:

0.000404

Gnomad AMR exome

AF:

0.00213

Gnomad ASJ exome

AF:

0.000703

Gnomad EAS exome

AF:

0.000213

Gnomad SAS exome

AF:

0.00218

Gnomad FIN exome

AF:

0.00679

Gnomad NFE exome

AF:

0.00520

Gnomad OTH exome

AF:

0.00314

GnomAD4 exome

AF:

0.00475

AC:

6392

AN:

1345900

Hom.:

Cov.:

AF XY:

0.00490

AC XY:

3254

AN XY:

663594

show subpopulations

Gnomad4 AFR exome

AF:

0.000759

Gnomad4 AMR exome

AF:

0.00290

Gnomad4 ASJ exome

AF:

0.000375

Gnomad4 EAS exome

AF:

0.000131

Gnomad4 SAS exome

AF:

0.00236

Gnomad4 FIN exome

AF:

0.00824

Gnomad4 NFE exome

AF:

0.00525

Gnomad4 OTH exome

AF:

0.00386

GnomAD4 genome

AF:

0.00397

AC:

604

AN:

152100

Hom.:

Cov.:

AF XY:

0.00374

AC XY:

278

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.000698

Gnomad4 AMR

AF:

0.00308

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00228

Gnomad4 FIN

AF:

0.00868

Gnomad4 NFE

AF:

0.00584

Gnomad4 OTH

AF:

0.0104

Alfa

AF:

0.00343

Hom.:

Bravo

AF:

0.00330

Asia WGS

AF:

0.00173

AC:

AN:

3472

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

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2024

PET117: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

DANN

Benign

0.93

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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