Variant chr2-218659583-G-A 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 NM_001379659.1(ZNF142):c.-576C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.056 in 152,316 control chromosomes in the GnomAD database, including 337 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.056 ( 337 hom., cov: 32)

Exomes 𝑓: 0.047 ( 0 hom. )

Consequence

ZNF142
NM_001379659.1 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.01

Variant links:

Genes affected

ZNF142 (HGNC:12927): (zinc finger protein 142) The protein encoded by this gene belongs to the Kruppel family of C2H2-type zinc finger proteins. It contains 31 C2H2-type zinc fingers and may be involved in transcriptional regulation. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2013]

ZNF142 links:

BCS1L (HGNC:1020): (BCS1 homolog, ubiquinol-cytochrome c reductase complex chaperone) This gene encodes a homolog of the S. cerevisiae bcs1 protein which is involved in the assembly of complex III of the mitochondrial respiratory chain. The encoded protein does not contain a mitochondrial targeting sequence but experimental studies confirm that it is imported into mitochondria. Mutations in this gene are associated with mitochondrial complex III deficiency and the GRACILE syndrome. Several alternatively spliced transcripts encoding two different isoforms have been described. [provided by RefSeq, Jan 2016]

BCS1L links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 2-218659583-G-A is Benign according to our data. Variant chr2-218659583-G-A is described in ClinVar as [Benign]. Clinvar id is 1262585.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF142	NM_001379659.1 linkuse as main transcript	c.-576C>T		5_prime_UTR_variant	1/11	ENST00000411696.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF142	ENST00000411696.7 linkuse as main transcript	c.-576C>T		5_prime_UTR_variant	1/11	5	NM_001379659.1	P1

Frequencies

GnomAD3 genomes

AF:

0.0560

AC:

8515

AN:

152112

Hom.:

336

Cov.:

show subpopulations

Gnomad AFR

AF:

0.106

Gnomad AMI

AF:

0.0230

Gnomad AMR

AF:

0.0312

Gnomad ASJ

AF:

0.0337

Gnomad EAS

AF:

0.117

Gnomad SAS

AF:

0.0437

Gnomad FIN

AF:

0.0271

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0339

Gnomad OTH

AF:

0.0507

GnomAD4 exome

AF:

0.0465

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0690

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.167

Gnomad4 NFE exome

AF:

0.0286

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0560

AC:

8530

AN:

152230

Hom.:

337

Cov.:

AF XY:

0.0549

AC XY:

4088

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.106

Gnomad4 AMR

AF:

0.0313

Gnomad4 ASJ

AF:

0.0337

Gnomad4 EAS

AF:

0.118

Gnomad4 SAS

AF:

0.0437

Gnomad4 FIN

AF:

0.0271

Gnomad4 NFE

AF:

0.0339

Gnomad4 OTH

AF:

0.0502

Alfa

AF:

0.0415

Hom.:

Bravo

AF:

0.0588

Asia WGS

AF:

0.0690

AC:

239

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

Apr 02, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

DANN

Benign

0.75

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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