Variant chr15-43361451-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001372080.1(ZSCAN29):c.2181C>T(p.Ile727=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0673 in 1,614,122 control chromosomes in the GnomAD database, including 4,165 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.053 ( 319 hom., cov: 32)

Exomes 𝑓: 0.069 ( 3846 hom. )

Consequence

ZSCAN29
NM_001372080.1 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00

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 -14 ACMG points.

BP4

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

BP6

Variant 15-43361451-G-A is Benign according to our data. Variant chr15-43361451-G-A is described in ClinVar as [Benign]. Clinvar id is 3060359.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=0 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.077 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
ZSCAN29	NM_001372080.1 linkuse as main transcript	c.2181C>T	p.Ile727=	synonymous_variant	6/6	ENST00000684362.1
ZSCAN29	NM_152455.4 linkuse as main transcript	c.2181C>T	p.Ile727=	synonymous_variant	5/5
ZSCAN29	XM_047432187.1 linkuse as main transcript	c.2181C>T	p.Ile727=	synonymous_variant	6/6
ZSCAN29	XM_047432188.1 linkuse as main transcript	c.1203C>T	p.Ile401=	synonymous_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZSCAN29	ENST00000684362.1 linkuse as main transcript	c.2181C>T	p.Ile727=	synonymous_variant	6/6		NM_001372080.1	P1	Q8IWY8-1

Frequencies

GnomAD3 genomes

AF:

0.0532

AC:

8094

AN:

152142

Hom.:

319

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0157

Gnomad AMI

AF:

0.0691

Gnomad AMR

AF:

0.0652

Gnomad ASJ

AF:

0.0829

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0244

Gnomad FIN

AF:

0.0432

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.0788

Gnomad OTH

AF:

0.0614

GnomAD3 exomes

AF:

0.0562

AC:

14122

AN:

251462

Hom.:

492

AF XY:

0.0568

AC XY:

7720

AN XY:

135902

show subpopulations

Gnomad AFR exome

AF:

0.0140

Gnomad AMR exome

AF:

0.0513

Gnomad ASJ exome

AF:

0.0801

Gnomad EAS exome

AF:

0.000272

Gnomad SAS exome

AF:

0.0300

Gnomad FIN exome

AF:

0.0472

Gnomad NFE exome

AF:

0.0786

Gnomad OTH exome

AF:

0.0701

GnomAD4 exome

AF:

0.0688

AC:

100524

AN:

1461862

Hom.:

3846

Cov.:

AF XY:

0.0681

AC XY:

49526

AN XY:

727236

show subpopulations

Gnomad4 AFR exome

AF:

0.0125

Gnomad4 AMR exome

AF:

0.0532

Gnomad4 ASJ exome

AF:

0.0823

Gnomad4 EAS exome

AF:

0.000302

Gnomad4 SAS exome

AF:

0.0313

Gnomad4 FIN exome

AF:

0.0486

Gnomad4 NFE exome

AF:

0.0773

Gnomad4 OTH exome

AF:

0.0648

GnomAD4 genome

AF:

0.0531

AC:

8089

AN:

152260

Hom.:

319

Cov.:

AF XY:

0.0500

AC XY:

3721

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.0156

Gnomad4 AMR

AF:

0.0650

Gnomad4 ASJ

AF:

0.0829

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0251

Gnomad4 FIN

AF:

0.0432

Gnomad4 NFE

AF:

0.0788

Gnomad4 OTH

AF:

0.0607

Alfa

AF:

0.0721

Hom.:

266

Bravo

AF:

0.0538

Asia WGS

AF:

0.0140

AC:

AN:

3478

EpiCase

AF:

0.0836

EpiControl

AF:

0.0817

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

ZSCAN29-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 21, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

6.7

DANN

Benign

0.67

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over