Variant chr5-178712441-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The ENST00000335815.7(ZNF354A):c.1437A>C(p.Ser479=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 1,603,016 control chromosomes in the GnomAD database, including 67,273 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5534 hom., cov: 32)

Exomes 𝑓: 0.29 ( 61739 hom. )

Consequence

ZNF354A
ENST00000335815.7 synonymous

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.795

Variant links:

Genes affected

ZNF354A (HGNC:11628): (zinc finger protein 354A) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in cytosol; nucleolus; and nucleoplasm. Biomarker of in situ carcinoma and seminoma. [provided by Alliance of Genome Resources, Apr 2022]

ZNF354A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 5-178712441-T-G is Benign according to our data. Variant chr5-178712441-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 768053.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.795 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF354A	NM_005649.3 linkuse as main transcript	c.1437A>C	p.Ser479=	synonymous_variant	5/5	ENST00000335815.7	NP_005640.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF354A	ENST00000335815.7 linkuse as main transcript	c.1437A>C	p.Ser479=	synonymous_variant	5/5	1	NM_005649.3	ENSP00000337122	P1

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

39733

AN:

151132

Hom.:

5528

Cov.:

show subpopulations

Gnomad AFR

AF:

0.187

Gnomad AMI

AF:

0.156

Gnomad AMR

AF:

0.253

Gnomad ASJ

AF:

0.283

Gnomad EAS

AF:

0.329

Gnomad SAS

AF:

0.392

Gnomad FIN

AF:

0.386

Gnomad MID

AF:

0.293

Gnomad NFE

AF:

0.279

Gnomad OTH

AF:

0.249

GnomAD3 exomes

AF:

0.301

AC:

75039

AN:

249536

Hom.:

12044

AF XY:

0.306

AC XY:

41212

AN XY:

134796

show subpopulations

Gnomad AFR exome

AF:

0.189

Gnomad AMR exome

AF:

0.281

Gnomad ASJ exome

AF:

0.292

Gnomad EAS exome

AF:

0.329

Gnomad SAS exome

AF:

0.406

Gnomad FIN exome

AF:

0.385

Gnomad NFE exome

AF:

0.274

Gnomad OTH exome

AF:

0.300

GnomAD4 exome

AF:

0.286

AC:

414945

AN:

1451766

Hom.:

61739

Cov.:

AF XY:

0.289

AC XY:

208946

AN XY:

722186

show subpopulations

Gnomad4 AFR exome

AF:

0.189

Gnomad4 AMR exome

AF:

0.280

Gnomad4 ASJ exome

AF:

0.294

Gnomad4 EAS exome

AF:

0.304

Gnomad4 SAS exome

AF:

0.398

Gnomad4 FIN exome

AF:

0.381

Gnomad4 NFE exome

AF:

0.275

Gnomad4 OTH exome

AF:

0.287

GnomAD4 genome

AF:

0.263

AC:

39758

AN:

151250

Hom.:

5534

Cov.:

AF XY:

0.270

AC XY:

19992

AN XY:

73912

show subpopulations

Gnomad4 AFR

AF:

0.187

Gnomad4 AMR

AF:

0.253

Gnomad4 ASJ

AF:

0.283

Gnomad4 EAS

AF:

0.329

Gnomad4 SAS

AF:

0.393

Gnomad4 FIN

AF:

0.386

Gnomad4 NFE

AF:

0.279

Gnomad4 OTH

AF:

0.256

Alfa

AF:

0.210

Hom.:

692

Bravo

AF:

0.246

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Sep 17, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

9.1

DANN

Benign

0.58

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