chr1-203798808-C-T
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001395895.1(ZBED6):c.1286C>T(p.Ser429Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000506 in 1,383,810 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000051 ( 0 hom. )
Consequence
ZBED6
NM_001395895.1 missense
NM_001395895.1 missense
Scores
2
5
12
Clinical Significance
Conservation
PhyloP100: 1.07
Genes affected
ZBED6 (HGNC:33273): (zinc finger BED-type containing 6) The protein encoded by this transposon-derived intronless gene is a transcriptional repressor that binds to the consensus sequence 5'-GCTCGC-3'. The encoded protein has been shown to repress IGF2 transcription. This gene is located within the first intron of the ZC3H11A gene. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZBED6 | NM_001395895.1 | c.1286C>T | p.Ser429Leu | missense_variant | 1/17 | ENST00000550078.3 | |
ZC3H11A | NM_001376342.1 | c.-1587-2767C>T | intron_variant | ENST00000367210.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZBED6 | ENST00000550078.3 | c.1286C>T | p.Ser429Leu | missense_variant | 1/17 | 1 | NM_001395895.1 | P1 | |
ZC3H11A | ENST00000367210.3 | c.-1587-2767C>T | intron_variant | 1 | NM_001376342.1 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD3 exomes AF: 0.00000744 AC: 1AN: 134498Hom.: 0 AF XY: 0.0000137 AC XY: 1AN XY: 73256
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GnomAD4 exome AF: 0.00000506 AC: 7AN: 1383810Hom.: 0 Cov.: 33 AF XY: 0.00000586 AC XY: 4AN XY: 682850
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GnomAD4 genome Cov.: 33
GnomAD4 genome
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33
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9
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3478
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 07, 2023 | The c.1286C>T (p.S429L) alteration is located in exon 1 (coding exon 1) of the ZBED6 gene. This alteration results from a C to T substitution at nucleotide position 1286, causing the serine (S) at amino acid position 429 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Uncertain
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D;D;D;N
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Benign
T
Sift4G
Pathogenic
D
Vest4
MutPred
Loss of glycosylation at S429 (P = 0.0465);
MVP
ClinPred
D
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