Variant rs3917221 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001372080.1(ZSCAN29):c.595G>A(p.Gly199Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 1,614,042 control chromosomes in the GnomAD database, including 28,574 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.17 ( 2444 hom., cov: 32)

Exomes 𝑓: 0.18 ( 26130 hom. )

Consequence

ZSCAN29
NM_001372080.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.485

Variant links:

Genes affected

ZSCAN29 (HGNC:26673): (zinc finger and SCAN domain containing 29) Enables sequence-specific double-stranded 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]

ZSCAN29 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0012399852).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZSCAN29	NM_001372080.1 linkuse as main transcript	c.595G>A	p.Gly199Ser	missense_variant	4/6	ENST00000684362.1	NP_001359009.1
ZSCAN29	NM_152455.4 linkuse as main transcript	c.595G>A	p.Gly199Ser	missense_variant	3/5		NP_689668.3	Q8IWY8-1Q96AG1Q05BJ4
ZSCAN29	XM_047432187.1 linkuse as main transcript	c.595G>A	p.Gly199Ser	missense_variant	4/6		XP_047288143.1
ZSCAN29	XM_047432188.1 linkuse as main transcript	c.-384G>A		5_prime_UTR_variant	2/4		XP_047288144.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZSCAN29	ENST00000684362.1 linkuse as main transcript	c.595G>A	p.Gly199Ser	missense_variant	4/6		NM_001372080.1	ENSP00000507363.1		Q8IWY8-1

Frequencies

GnomAD3 genomes

AF:

0.172

AC:

26196

AN:

152058

Hom.:

2446

Cov.:

show subpopulations

Gnomad AFR

AF:

0.187

Gnomad AMI

AF:

0.117

Gnomad AMR

AF:

0.142

Gnomad ASJ

AF:

0.212

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.191

Gnomad FIN

AF:

0.121

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.188

Gnomad OTH

AF:

0.186

GnomAD3 exomes

AF:

0.161

AC:

40472

AN:

251432

Hom.:

3733

AF XY:

0.167

AC XY:

22746

AN XY:

135884

show subpopulations

Gnomad AFR exome

AF:

0.186

Gnomad AMR exome

AF:

0.101

Gnomad ASJ exome

AF:

0.206

Gnomad EAS exome

AF:

0.00250

Gnomad SAS exome

AF:

0.212

Gnomad FIN exome

AF:

0.126

Gnomad NFE exome

AF:

0.189

Gnomad OTH exome

AF:

0.178

GnomAD4 exome

AF:

0.183

AC:

267372

AN:

1461866

Hom.:

26130

Cov.:

AF XY:

0.185

AC XY:

134225

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.187

Gnomad4 AMR exome

AF:

0.106

Gnomad4 ASJ exome

AF:

0.208

Gnomad4 EAS exome

AF:

0.00149

Gnomad4 SAS exome

AF:

0.219

Gnomad4 FIN exome

AF:

0.128

Gnomad4 NFE exome

AF:

0.191

Gnomad4 OTH exome

AF:

0.181

GnomAD4 genome

AF:

0.172

AC:

26207

AN:

152176

Hom.:

2444

Cov.:

AF XY:

0.168

AC XY:

12496

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.187

Gnomad4 AMR

AF:

0.142

Gnomad4 ASJ

AF:

0.212

Gnomad4 EAS

AF:

0.00135

Gnomad4 SAS

AF:

0.190

Gnomad4 FIN

AF:

0.121

Gnomad4 NFE

AF:

0.188

Gnomad4 OTH

AF:

0.184

Alfa

AF:

0.186

Hom.:

5231

Bravo

AF:

0.173

TwinsUK

AF:

0.194

AC:

719

ALSPAC

AF:

0.187

AC:

721

ESP6500AA

AF:

0.192

AC:

845

ESP6500EA

AF:

0.189

AC:

1622

ExAC

AF:

0.165

AC:

20029

Asia WGS

AF:

0.0880

AC:

310

AN:

3478

EpiCase

AF:

0.194

EpiControl

AF:

0.192

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.67

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0097

T;.;T;T

Eigen

Benign

-0.65

Eigen_PC

Benign

-0.53

FATHMM_MKL

Benign

0.17

LIST_S2

Benign

0.68

T;T;T;T

MetaRNN

Benign

0.0012

T;T;T;T

MetaSVM

Benign

-0.92

MutationAssessor

Benign

0.95

L;.;.;.

PrimateAI

Benign

0.27

PROVEAN

Benign

-0.59

N;.;N;N

REVEL

Benign

0.046

Sift

Benign

0.57

T;.;T;T

Sift4G

Benign

0.59

T;T;T;T

Polyphen

0.0060

B;.;B;.

Vest4

0.096

MPC

0.094

ClinPred

0.0031

GERP RS

3.2

Varity_R

0.020

gMVP

0.16

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over