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GeneBe

15-43361451-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

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 (★).

Frequency

Genomes: 𝑓 0.053 ( 319 hom., cov: 32)
Exomes 𝑓: 0.069 ( 3846 hom. )

Consequence

ZSCAN29
NM_001372080.1 synonymous

Scores

2

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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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 criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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 UniProt
ZSCAN29NM_001372080.1 linkuse as main transcriptc.2181C>T p.Ile727= synonymous_variant 6/6 ENST00000684362.1
ZSCAN29NM_152455.4 linkuse as main transcriptc.2181C>T p.Ile727= synonymous_variant 5/5
ZSCAN29XM_047432187.1 linkuse as main transcriptc.2181C>T p.Ile727= synonymous_variant 6/6
ZSCAN29XM_047432188.1 linkuse as main transcriptc.1203C>T p.Ile401= synonymous_variant 4/4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZSCAN29ENST00000684362.1 linkuse as main transcriptc.2181C>T p.Ile727= synonymous_variant 6/6 NM_001372080.1 P1Q8IWY8-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0532
AC:
8094
AN:
152142
Hom.:
319
Cov.:
32
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.:
32
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0531
AC:
8089
AN:
152260
Hom.:
319
Cov.:
32
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:
47
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 submitterclinical testingPreventionGenetics, part of Exact SciencesOct 21, 2019This 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.

Other links and lift over

dbSNP: rs62019445; hg19: chr15-43653649; COSMIC: COSV67822609; COSMIC: COSV67822609; API