Variant X-104115002-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The ENST00000594199.3(SLC25A53):c.-31-9714G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000187 in 1,191,636 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 74 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000062 ( 0 hom., 1 hem., cov: 23)

Exomes 𝑓: 0.00020 ( 0 hom. 73 hem. )

Consequence

SLC25A53
ENST00000594199.3 intron

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.327

Variant links:

Genes affected

ZCCHC18 (HGNC:32459): (zinc finger CCHC-type containing 18) Predicted to enable metal ion binding activity. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZCCHC18 links:

SLC25A53 (HGNC:31894): (solute carrier family 25 member 53) Predicted to be located in mitochondrial inner membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC25A53 links:

ZCCHC18 (HGNC:):

ZCCHC18 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant X-104115002-C-T is Benign according to our data. Variant chrX-104115002-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2661108.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAdExome4 at 73 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZCCHC18	NM_001143978.3 linkuse as main transcript	c.891C>T	p.Phe297Phe	synonymous_variant	3/3	ENST00000650639.1	NP_001137450.1	P0CG32
SLC25A53	NM_001012755.5 linkuse as main transcript	c.-31-9714G>A		intron_variant		ENST00000594199.3	NP_001012773.2	Q5H9E4
ZCCHC18	XM_011531012.4 linkuse as main transcript	c.891C>T	p.Phe297Phe	synonymous_variant	3/3		XP_011529314.1	P0CG32
ZCCHC18	NR_026694.3 linkuse as main transcript	n.672-250C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ZCCHC18	ENST00000650639.1 linkuse as main transcript	c.891C>T	p.Phe297Phe	synonymous_variant	3/3		NM_001143978.3	ENSP00000498828.1	P0CG32
SLC25A53	ENST00000594199.3 linkuse as main transcript	c.-31-9714G>A		intron_variant		1	NM_001012755.5	ENSP00000468980.1	Q5H9E4
ZCCHC18	ENST00000537356.3 linkuse as main transcript	c.891C>T	p.Phe297Phe	synonymous_variant	2/2	5		ENSP00000473824.1	P0CG32
ZCCHC18	ENST00000422784.5 linkuse as main transcript	n.651-250C>T		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0000625

AC:

AN:

112013

Hom.:

Cov.:

AF XY:

0.0000293

AC XY:

AN XY:

34167

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000132

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000408

AC:

AN:

146994

Hom.:

AF XY:

0.0000441

AC XY:

AN XY:

45356

show subpopulations

Gnomad AFR exome

AF:

0.000104

Gnomad AMR exome

AF:

0.0000421

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000646

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000200

AC:

216

AN:

1079623

Hom.:

Cov.:

AF XY:

0.000208

AC XY:

AN XY:

351473

show subpopulations

Gnomad4 AFR exome

AF:

0.0000386

Gnomad4 AMR exome

AF:

0.0000309

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000250

Gnomad4 OTH exome

AF:

0.000132

GnomAD4 genome

AF:

0.0000625

AC:

AN:

112013

Hom.:

Cov.:

AF XY:

0.0000293

AC XY:

AN XY:

34167

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000132

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000868

Hom.:

Bravo

AF:

0.0000756

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

Mar 01, 2022

ZCCHC18: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.85

DANN

Benign

0.36

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