10-38054785-T-G
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006954.2(ZNF33A):āc.661T>Gā(p.Tyr221Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,396 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 33)
Exomes š: 6.8e-7 ( 0 hom. )
Consequence
ZNF33A
NM_006954.2 missense
NM_006954.2 missense
Scores
6
13
Clinical Significance
Conservation
PhyloP100: 0.215
Genes affected
ZNF33A (HGNC:13096): (zinc finger protein 33A) Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF33A | NM_006954.2 | c.661T>G | p.Tyr221Asp | missense_variant | 5/5 | ENST00000432900.7 | NP_008885.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF33A | ENST00000432900.7 | c.661T>G | p.Tyr221Asp | missense_variant | 5/5 | 1 | NM_006954.2 | ENSP00000402467.3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461396Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 726990
GnomAD4 exome
AF:
AC:
1
AN:
1461396
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
726990
Gnomad4 AFR exome
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Gnomad4 ASJ exome
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GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
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 | Aug 04, 2021 | The c.661T>G (p.Y221D) alteration is located in exon 5 (coding exon 4) of the ZNF33A gene. This alteration results from a T to G substitution at nucleotide position 661, causing the tyrosine (Y) at amino acid position 221 to be replaced by an aspartic acid (D). 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
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.;.;.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T;T;T
M_CAP
Benign
T
MetaRNN
Uncertain
D;D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;.;.;.;M
PrimateAI
Benign
T
PROVEAN
Uncertain
.;.;.;.;D
REVEL
Benign
Sift
Uncertain
.;.;.;.;D
Sift4G
Uncertain
T;D;T;T;T
Polyphen
0.14
.;.;.;.;B
Vest4
MutPred
0.73
.;.;.;.;Gain of disorder (P = 0.0088);
MVP
MPC
0.22
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.