Variant 19-56207128-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001358413.3(ZSCAN5C):c.454G>A(p.Ala152Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00418 in 774,286 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0038 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0043 ( 14 hom. )

Consequence

ZSCAN5C
NM_001358413.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.04

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:

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 (MetaRNN=0.005938709).

BP6

Variant 19-56207128-G-A is Benign according to our data. Variant chr19-56207128-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2650556.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSCAN5C	NM_001358413.3 linkuse as main transcript	c.454G>A	p.Ala152Thr	missense_variant	3/5	ENST00000534327.7	NP_001345342.1
ZSCAN5C	XM_047439230.1 linkuse as main transcript	c.454G>A	p.Ala152Thr	missense_variant	2/4		XP_047295186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZSCAN5C	ENST00000534327.7 linkuse as main transcript	c.454G>A	p.Ala152Thr	missense_variant	3/5	5	NM_001358413.3	ENSP00000435234.1		A6NGD5

Frequencies

GnomAD3 genomes

AF:

0.00375

AC:

570

AN:

151820

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00146

Gnomad AMI

AF:

0.00549

Gnomad AMR

AF:

0.00256

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000829

Gnomad FIN

AF:

0.00557

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00581

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00372

AC:

882

AN:

237370

Hom.:

AF XY:

0.00357

AC XY:

460

AN XY:

128676

show subpopulations

Gnomad AFR exome

AF:

0.00181

Gnomad AMR exome

AF:

0.00142

Gnomad ASJ exome

AF:

0.000203

Gnomad EAS exome

AF:

0.0000563

Gnomad SAS exome

AF:

0.00113

Gnomad FIN exome

AF:

0.00493

Gnomad NFE exome

AF:

0.00605

Gnomad OTH exome

AF:

0.00424

GnomAD4 exome

AF:

0.00429

AC:

2667

AN:

622348

Hom.:

Cov.:

AF XY:

0.00409

AC XY:

1384

AN XY:

338566

show subpopulations

Gnomad4 AFR exome

AF:

0.00159

Gnomad4 AMR exome

AF:

0.00164

Gnomad4 ASJ exome

AF:

0.000240

Gnomad4 EAS exome

AF:

0.0000556

Gnomad4 SAS exome

AF:

0.00120

Gnomad4 FIN exome

AF:

0.00504

Gnomad4 NFE exome

AF:

0.00591

Gnomad4 OTH exome

AF:

0.00473

GnomAD4 genome

AF:

0.00375

AC:

570

AN:

151938

Hom.:

Cov.:

AF XY:

0.00369

AC XY:

274

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.00145

Gnomad4 AMR

AF:

0.00255

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000830

Gnomad4 FIN

AF:

0.00557

Gnomad4 NFE

AF:

0.00581

Gnomad4 OTH

AF:

0.00332

Alfa

AF:

0.00225

Hom.:

Bravo

AF:

0.00383

ExAC

AF:

0.00346

AC:

420

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, 2023

ZSCAN5C: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.71

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.0056

T;T

Eigen

Benign

-0.82

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.034

LIST_S2

Benign

0.35

.;T

M_CAP

Benign

0.00043

MetaRNN

Benign

0.0059

T;T

MetaSVM

Benign

-0.90

MutationTaster

Benign

1.0

N;N

PROVEAN

Benign

-1.3

N;N

REVEL

Benign

0.024

Sift

Benign

0.11

T;T

Sift4G

Benign

0.32

T;T

Vest4

0.076

MVP

0.092

MPC

0.0071

ClinPred

0.0046

GERP RS

-0.16

Varity_R

0.050

gMVP

0.052

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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