18-48029435-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000590800.6(ZBTB7C):c.1685C>T(p.Ala562Val) variant causes a missense change. The variant allele was found at a frequency of 0.000247 in 1,591,434 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0012 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00014 ( 2 hom. )
Consequence
ZBTB7C
ENST00000590800.6 missense
ENST00000590800.6 missense
Scores
1
2
15
Clinical Significance
Conservation
PhyloP100: 4.60
Genes affected
ZBTB7C (HGNC:31700): (zinc finger and BTB domain containing 7C) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of cell population proliferation. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0055345893).
BP6
Variant 18-48029435-G-A is Benign according to our data. Variant chr18-48029435-G-A is described in ClinVar as [Benign]. Clinvar id is 723710.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 185 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZBTB7C | NM_001318841.2 | c.1685C>T | p.Ala562Val | missense_variant | 5/5 | ENST00000590800.6 | NP_001305770.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZBTB7C | ENST00000590800.6 | c.1685C>T | p.Ala562Val | missense_variant | 5/5 | 1 | NM_001318841.2 | ENSP00000467877 | P1 | |
ZBTB7C | ENST00000535628.6 | c.1685C>T | p.Ala562Val | missense_variant | 3/3 | 1 | ENSP00000439781 | P1 | ||
ZBTB7C | ENST00000586438.5 | c.1685C>T | p.Ala562Val | missense_variant | 3/3 | 1 | ENSP00000468254 | P1 | ||
ZBTB7C | ENST00000588982.5 | c.1685C>T | p.Ala562Val | missense_variant | 4/4 | 1 | ENSP00000468782 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00121 AC: 184AN: 152120Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000297 AC: 64AN: 215400Hom.: 1 AF XY: 0.000226 AC XY: 27AN XY: 119478
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GnomAD4 exome AF: 0.000145 AC: 208AN: 1439206Hom.: 2 Cov.: 32 AF XY: 0.000117 AC XY: 84AN XY: 715692
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GnomAD4 genome AF: 0.00122 AC: 185AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.00107 AC XY: 80AN XY: 74426
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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 | Labcorp Genetics (formerly Invitae), Labcorp | May 21, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
.;.;.;T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;N;N
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;.;.;.
REVEL
Benign
Sift
Benign
T;.;.;.
Sift4G
Benign
T;T;T;T
Polyphen
B;B;B;B
Vest4
MVP
MPC
0.41
ClinPred
T
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at