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15-43361124-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.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

2

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]

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 15-43361124-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_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=1.31 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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 UniProt
ZSCAN29NM_001372080.1 linkuse as main transcriptc.2508C>T p.His836= synonymous_variant 6/6 ENST00000684362.1
ZSCAN29NM_152455.4 linkuse as main transcriptc.2508C>T p.His836= synonymous_variant 5/5
ZSCAN29XM_047432187.1 linkuse as main transcriptc.2508C>T p.His836= synonymous_variant 6/6
ZSCAN29XM_047432188.1 linkuse as main transcriptc.1530C>T p.His510= synonymous_variant 4/4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZSCAN29ENST00000684362.1 linkuse as main transcriptc.2508C>T p.His836= synonymous_variant 6/6 NM_001372080.1 P1Q8IWY8-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.173
AC:
26255
AN:
152042
Hom.:
2453
Cov.:
32
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.:
32
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.173
AC:
26266
AN:
152160
Hom.:
2451
Cov.:
32
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 submitterclinical testingGeneDxNov 06, 2020- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.54
Cadd
Benign
11
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.

Other links and lift over

dbSNP: rs35278805; hg19: chr15-43653322; COSMIC: COSV67822215; COSMIC: COSV67822215; API