chr19-57678455-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_152677.4(ZSCAN4):c.852G>C(p.Glu284Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00418 in 1,614,124 control chromosomes in the GnomAD database, including 238 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.022 ( 133 hom., cov: 32)
Exomes 𝑓: 0.0023 ( 105 hom. )
Consequence
ZSCAN4
NM_152677.4 missense
NM_152677.4 missense
Scores
17
Clinical Significance
Conservation
PhyloP100: 1.32
Genes affected
ZSCAN4 (HGNC:23709): (zinc finger and SCAN domain containing 4) The ZSCAN4 gene encodes a protein involved in telomere maintenance and with a key role in the critical feature of mouse embryonic stem (ES) cells, namely, defying cellular senescence and maintaining normal karyotype for many cell divisions in culture (Zalzman et al., 2010 [PubMed 20336070]).[supplied by OMIM, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0027216375).
BP6
?
Variant 19-57678455-G-C is Benign according to our data. Variant chr19-57678455-G-C is described in ClinVar as [Benign]. Clinvar id is 777511.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0736 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZSCAN4 | NM_152677.4 | c.852G>C | p.Glu284Asp | missense_variant | 5/5 | ENST00000318203.9 | |
ZSCAN4 | NM_001384833.1 | c.852G>C | p.Glu284Asp | missense_variant | 7/7 | ||
ZSCAN4 | XM_017026458.1 | c.852G>C | p.Glu284Asp | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZSCAN4 | ENST00000318203.9 | c.852G>C | p.Glu284Asp | missense_variant | 5/5 | 2 | NM_152677.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0218 AC: 3310AN: 152130Hom.: 132 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00617 AC: 1550AN: 251318Hom.: 52 AF XY: 0.00452 AC XY: 614AN XY: 135834
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GnomAD4 exome AF: 0.00234 AC: 3426AN: 1461876Hom.: 105 Cov.: 31 AF XY: 0.00205 AC XY: 1491AN XY: 727234
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GnomAD4 genome ? AF: 0.0218 AC: 3323AN: 152248Hom.: 133 Cov.: 32 AF XY: 0.0210 AC XY: 1561AN XY: 74438
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ESP6500AA
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329
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ExAC
?
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905
Asia WGS
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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 | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N;.
REVEL
Benign
Sift
Benign
T;.
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MutPred
Gain of glycosylation at S285 (P = 0.1185);Gain of glycosylation at S285 (P = 0.1185);
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at