chr2-179769545-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152520.6(ZNF385B):c.256C>T(p.Pro86Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000164 in 1,461,770 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.000016 ( 0 hom. )
Consequence
ZNF385B
NM_152520.6 missense
NM_152520.6 missense
Scores
1
12
Clinical Significance
Conservation
PhyloP100: 4.07
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.06417394).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF385B | NM_152520.6 | c.256C>T | p.Pro86Ser | missense_variant | 3/10 | ENST00000410066.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF385B | ENST00000410066.7 | c.256C>T | p.Pro86Ser | missense_variant | 3/10 | 1 | NM_152520.6 | P1 | |
ZNF385B | ENST00000451732.6 | c.256C>T | p.Pro86Ser | missense_variant | 3/3 | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD3 exomes AF: 0.0000719 AC: 18AN: 250486Hom.: 0 AF XY: 0.0000591 AC XY: 8AN XY: 135472
GnomAD3 exomes
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GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461770Hom.: 0 Cov.: 32 AF XY: 0.0000165 AC XY: 12AN XY: 727186
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
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?
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4
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 | Jul 12, 2023 | The c.211C>T (p.P71S) alteration is located in exon 3 (coding exon 1) of the ZNF385B gene. This alteration results from a C to T substitution at nucleotide position 211, causing the proline (P) at amino acid position 71 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N
PrimateAI
Benign
T
REVEL
Benign
Polyphen
0.0
.;B;.
MutPred
0.25
.;Loss of catalytic residue at P71 (P = 0.0061);.;
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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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