Variant chr6-28329536-T-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_030899.5(ZSCAN31):c.148A>T(p.Thr50Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 1,613,804 control chromosomes in the GnomAD database, including 22,147 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 0.19 ( 3639 hom., cov: 32)

Exomes 𝑓: 0.15 ( 18508 hom. )

Consequence

ZSCAN31
NM_030899.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.779

Variant links:

Genes affected

ZSCAN31 (HGNC:14097): (zinc finger and SCAN domain containing 31) This gene encodes a protein containing multiple C2H2-type zinc finger motifs. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ZSCAN31 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=0.0044205785).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZSCAN31	NM_030899.5 linkuse as main transcript	c.148A>T	p.Thr50Ser	missense_variant	2/4	ENST00000344279.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZSCAN31	ENST00000344279.11 linkuse as main transcript	c.148A>T	p.Thr50Ser	missense_variant	2/4	1	NM_030899.5	P1	Q96LW9-1

Frequencies

GnomAD3 genomes

AF:

0.192

AC:

29206

AN:

151796

Hom.:

3629

Cov.:

show subpopulations

Gnomad AFR

AF:

0.348

Gnomad AMI

AF:

0.142

Gnomad AMR

AF:

0.165

Gnomad ASJ

AF:

0.127

Gnomad EAS

AF:

0.127

Gnomad SAS

AF:

0.0925

Gnomad FIN

AF:

0.0565

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.142

Gnomad OTH

AF:

0.180

GnomAD3 exomes

AF:

0.138

AC:

34781

AN:

251452

Hom.:

2969

AF XY:

0.133

AC XY:

18100

AN XY:

135894

show subpopulations

Gnomad AFR exome

AF:

0.358

Gnomad AMR exome

AF:

0.139

Gnomad ASJ exome

AF:

0.129

Gnomad EAS exome

AF:

0.128

Gnomad SAS exome

AF:

0.0948

Gnomad FIN exome

AF:

0.0607

Gnomad NFE exome

AF:

0.136

Gnomad OTH exome

AF:

0.129

GnomAD4 exome

AF:

0.152

AC:

221882

AN:

1461890

Hom.:

18508

Cov.:

AF XY:

0.149

AC XY:

108269

AN XY:

727244

show subpopulations

Gnomad4 AFR exome

AF:

0.360

Gnomad4 AMR exome

AF:

0.140

Gnomad4 ASJ exome

AF:

0.129

Gnomad4 EAS exome

AF:

0.152

Gnomad4 SAS exome

AF:

0.0947

Gnomad4 FIN exome

AF:

0.0629

Gnomad4 NFE exome

AF:

0.156

Gnomad4 OTH exome

AF:

0.150

GnomAD4 genome

AF:

0.192

AC:

29233

AN:

151914

Hom.:

3639

Cov.:

AF XY:

0.185

AC XY:

13707

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.348

Gnomad4 AMR

AF:

0.165

Gnomad4 ASJ

AF:

0.127

Gnomad4 EAS

AF:

0.127

Gnomad4 SAS

AF:

0.0928

Gnomad4 FIN

AF:

0.0565

Gnomad4 NFE

AF:

0.142

Gnomad4 OTH

AF:

0.178

Alfa

AF:

0.135

Hom.:

1149

Bravo

AF:

0.211

TwinsUK

AF:

0.176

AC:

652

ALSPAC

AF:

0.164

AC:

633

ESP6500AA

AF:

0.335

AC:

1478

ESP6500EA

AF:

0.145

AC:

1247

ExAC

AF:

0.140

AC:

17012

Asia WGS

AF:

0.111

AC:

387

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.22

BayesDel_addAF

Benign

-0.72

BayesDel_noAF

Benign

-0.67

CADD

Benign

DANN

Benign

0.88

DEOGEN2

Benign

0.0019

T;T;T;T;.;T;T;T;.;T

Eigen

Benign

-0.84

Eigen_PC

Benign

-0.80

FATHMM_MKL

Benign

0.14

LIST_S2

Benign

0.035

.;.;.;T;T;T;T;T;T;T

MetaRNN

Benign

0.0044

T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-0.90

MutationAssessor

Benign

0.87

L;L;L;L;.;.;.;.;.;.

MutationTaster

Benign

1.0

P;P;P;P;P

PrimateAI

Benign

0.47

PROVEAN

Benign

-1.9

N;N;N;N;N;N;N;N;N;D

REVEL

Benign

0.048

Sift

Benign

0.27

T;T;T;T;T;T;T;T;T;T

Sift4G

Benign

0.20

T;T;T;T;T;.;.;.;.;T

Polyphen

0.046

B;B;B;B;.;.;.;.;.;.

Vest4

0.043

MutPred

0.49

Loss of phosphorylation at T50 (P = 0.0447);Loss of phosphorylation at T50 (P = 0.0447);Loss of phosphorylation at T50 (P = 0.0447);Loss of phosphorylation at T50 (P = 0.0447);Loss of phosphorylation at T50 (P = 0.0447);Loss of phosphorylation at T50 (P = 0.0447);Loss of phosphorylation at T50 (P = 0.0447);Loss of phosphorylation at T50 (P = 0.0447);Loss of phosphorylation at T50 (P = 0.0447);Loss of phosphorylation at T50 (P = 0.0447);

MPC

0.090

ClinPred

0.0034

GERP RS

-1.0

Varity_R

0.072

gMVP

0.068

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over