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

Variant summary

Our verdict is Benign. The variant received -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

Publications

0 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001358413.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSCAN5C	NM_001358413.3	MANE Select	c.792G>C	p.Val264Val	synonymous	Exon 5 of 5	NP_001345342.1	A6NGD5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSCAN5C	ENST00000534327.7	TSL:5 MANE Select	c.792G>C	p.Val264Val	synonymous	Exon 5 of 5	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

GnomAD2 exomes

AF:

0.000718

AC:

178

AN:

247832

AF XY:

0.000796

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 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

African (AFR)

AF:

0.00163

AC:

AN:

31812

American (AMR)

AF:

0.000450

AC:

AN:

44480

Ashkenazi Jewish (ASJ)

AF:

0.000622

AC:

AN:

25740

East Asian (EAS)

AF:

0.0000508

AC:

AN:

39400

South Asian (SAS)

AF:

0.000789

AC:

AN:

84970

European-Finnish (FIN)

AF:

0.000601

AC:

AN:

49952

Middle Eastern (MID)

AF:

0.000883

AC:

AN:

5662

European-Non Finnish (NFE)

AF:

0.000959

AC:

1017

AN:

1059946

Other (OTH)

AF:

0.000825

AC:

AN:

58196

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.446

Heterozygous variant carriers

100

150

200

250

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

120

160

200

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00115

AC:

175

AN:

151988

Hom.:

Cov.:

AF XY:

0.00105

AC XY:

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.00187

AC:

AN:

41274

American (AMR)

AF:

0.000392

AC:

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.000865

AC:

AN:

3470

East Asian (EAS)

AF:

0.000193

AC:

AN:

5180

South Asian (SAS)

AF:

0.000622

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.000283

AC:

AN:

10598

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00119

AC:

AN:

68030

Other (OTH)

AF:

0.000473

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.457

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000836

Hom.:

Bravo

AF:

0.00133

EpiCase

AF:

0.00147

EpiControl

AF:

0.000534

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.22

(source)

DANN

Benign

0.64

PhyloP100

-0.42

Mutation Taster

=100/0

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over