Variant 15-43361124-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001372080.1(ZSCAN29):c.2508C>T(p.His836=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 1,611,554 control chromosomes in the GnomAD database, including 28,628 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.17 ( 2451 hom., cov: 32)

Exomes 𝑓: 0.18 ( 26177 hom. )

Consequence

ZSCAN29
NM_001372080.1 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.31

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 15-43361124-G-A is Benign according to our data. Variant chr15-43361124-G-A is described in ClinVar as [Benign]. Clinvar id is 1228847.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.31 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
ZSCAN29	NM_001372080.1 linkuse as main transcript	c.2508C>T	p.His836=	synonymous_variant	6/6	ENST00000684362.1
ZSCAN29	NM_152455.4 linkuse as main transcript	c.2508C>T	p.His836=	synonymous_variant	5/5
ZSCAN29	XM_047432187.1 linkuse as main transcript	c.2508C>T	p.His836=	synonymous_variant	6/6
ZSCAN29	XM_047432188.1 linkuse as main transcript	c.1530C>T	p.His510=	synonymous_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZSCAN29	ENST00000684362.1 linkuse as main transcript	c.2508C>T	p.His836=	synonymous_variant	6/6		NM_001372080.1	P1	Q8IWY8-1

Frequencies

GnomAD3 genomes

AF:

0.173

AC:

26255

AN:

152042

Hom.:

2453

Cov.:

show subpopulations

Gnomad AFR

AF:

0.188

Gnomad AMI

AF:

0.118

Gnomad AMR

AF:

0.142

Gnomad ASJ

AF:

0.213

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.197

Gnomad FIN

AF:

0.121

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.188

Gnomad OTH

AF:

0.187

GnomAD3 exomes

AF:

0.162

AC:

40556

AN:

251038

Hom.:

3759

AF XY:

0.168

AC XY:

22806

AN XY:

135668

show subpopulations

Gnomad AFR exome

AF:

0.186

Gnomad AMR exome

AF:

0.101

Gnomad ASJ exome

AF:

0.206

Gnomad EAS exome

AF:

0.00256

Gnomad SAS exome

AF:

0.217

Gnomad FIN exome

AF:

0.126

Gnomad NFE exome

AF:

0.189

Gnomad OTH exome

AF:

0.178

GnomAD4 exome

AF:

0.183

AC:

267321

AN:

1459394

Hom.:

26177

Cov.:

AF XY:

0.185

AC XY:

134185

AN XY:

725438

show subpopulations

Gnomad4 AFR exome

AF:

0.187

Gnomad4 AMR exome

AF:

0.106

Gnomad4 ASJ exome

AF:

0.208

Gnomad4 EAS exome

AF:

0.00152

Gnomad4 SAS exome

AF:

0.224

Gnomad4 FIN exome

AF:

0.128

Gnomad4 NFE exome

AF:

0.191

Gnomad4 OTH exome

AF:

0.181

GnomAD4 genome

AF:

0.173

AC:

26266

AN:

152160

Hom.:

2451

Cov.:

AF XY:

0.168

AC XY:

12524

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.188

Gnomad4 AMR

AF:

0.142

Gnomad4 ASJ

AF:

0.213

Gnomad4 EAS

AF:

0.00135

Gnomad4 SAS

AF:

0.196

Gnomad4 FIN

AF:

0.121

Gnomad4 NFE

AF:

0.188

Gnomad4 OTH

AF:

0.185

Alfa

AF:

0.174

Hom.:

1266

Bravo

AF:

0.173

Asia WGS

AF:

0.0920

AC:

325

AN:

3478

EpiCase

AF:

0.194

EpiControl

AF:

0.192

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 06, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

DANN

Benign

0.66

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