Genetic Variant ZSCAN5C:p.Val264Val (chr19-56208501-G-C) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001358413.3(ZSCAN5C):c.792G>C(p.Val264Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000923 in 1,552,146 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0012 ( 1 hom., cov: 32)

Exomes 𝑓: 0.00090 ( 2 hom. )

Consequence

ZSCAN5C
NM_001358413.3 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.418

Variant links:

Genes affected

ZSCAN5C (HGNC:34294): (zinc finger and SCAN domain containing 5C) 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. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZSCAN5C links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant 19-56208501-G-C is Benign according to our data. Variant chr19-56208501-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 2650557.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.418 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSCAN5C	NM_001358413.3 link	c.792G>C	p.Val264Val	synonymous_variant	Exon 5 of 5	ENST00000534327.7	NP_001345342.1
ZSCAN5C	XM_047439230.1 link	c.789G>C	p.Val263Val	synonymous_variant	Exon 4 of 4		XP_047295186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSCAN5C	ENST00000534327.7 link	c.792G>C	p.Val264Val	synonymous_variant	Exon 5 of 5	5	NM_001358413.3	ENSP00000435234.1		A6NGD5

Frequencies

GnomAD3 genomes

AF:

0.00115

AC:

174

AN:

151870

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00185

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000393

Gnomad ASJ

AF:

0.000865

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.000283

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00119

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.000718

AC:

178

AN:

247832

Hom.:

AF XY:

0.000796

AC XY:

107

AN XY:

134500

show subpopulations

Gnomad AFR exome

AF:

0.00103

Gnomad AMR exome

AF:

0.000378

Gnomad ASJ exome

AF:

0.000497

Gnomad EAS exome

AF:

0.0000546

Gnomad SAS exome

AF:

0.000753

Gnomad FIN exome

AF:

0.000350

Gnomad NFE exome

AF:

0.000930

Gnomad OTH exome

AF:

0.00132

GnomAD4 exome

AF:

0.000898

AC:

1257

AN:

1400158

Hom.:

Cov.:

AF XY:

0.000929

AC XY:

650

AN XY:

699898

show subpopulations

Gnomad4 AFR exome

AF:

0.00163

Gnomad4 AMR exome

AF:

0.000450

Gnomad4 ASJ exome

AF:

0.000622

Gnomad4 EAS exome

AF:

0.0000508

Gnomad4 SAS exome

AF:

0.000789

Gnomad4 FIN exome

AF:

0.000601

Gnomad4 NFE exome

AF:

0.000959

Gnomad4 OTH exome

AF:

0.000825

GnomAD4 genome

AF:

0.00115

AC:

175

AN:

151988

Hom.:

Cov.:

AF XY:

0.00105

AC XY:

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.00187

Gnomad4 AMR

AF:

0.000392

Gnomad4 ASJ

AF:

0.000865

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.000622

Gnomad4 FIN

AF:

0.000283

Gnomad4 NFE

AF:

0.00119

Gnomad4 OTH

AF:

0.000473

Alfa

AF:

0.000836

Hom.:

Bravo

AF:

0.00133

EpiCase

AF:

0.00147

EpiControl

AF:

0.000534

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

May 01, 2022

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ZSCAN5C: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.22

DANN

Benign

0.64

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