rs59922637
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_201269.3(ZNF644):āc.2608A>Gā(p.Thr870Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00239 in 1,613,938 control chromosomes in the GnomAD database, including 84 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.013 ( 39 hom., cov: 32)
Exomes š: 0.0013 ( 45 hom. )
Consequence
ZNF644
NM_201269.3 missense
NM_201269.3 missense
Scores
3
14
Clinical Significance
Conservation
PhyloP100: 3.88
Genes affected
ZNF644 (HGNC:29222): (zinc finger protein 644) The protein encoded by this gene is a zinc finger transcription factor that may play a role in eye development. Defects in this gene have been associated with high myopia. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]
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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=0.004046917).
BP6
?
Variant 1-90938746-T-C is Benign according to our data. Variant chr1-90938746-T-C is described in ClinVar as [Benign]. Clinvar id is 780246.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0126 (1924/152238) while in subpopulation AFR AF= 0.0438 (1819/41546). AF 95% confidence interval is 0.0421. There are 39 homozygotes in gnomad4. There are 917 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 1924 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF644 | NM_201269.3 | c.2608A>G | p.Thr870Ala | missense_variant | 3/6 | ENST00000337393.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF644 | ENST00000337393.10 | c.2608A>G | p.Thr870Ala | missense_variant | 3/6 | 1 | NM_201269.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0126 AC: 1917AN: 152120Hom.: 39 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00336 AC: 842AN: 250690Hom.: 22 AF XY: 0.00242 AC XY: 328AN XY: 135502
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GnomAD4 exome AF: 0.00132 AC: 1927AN: 1461700Hom.: 45 Cov.: 33 AF XY: 0.00110 AC XY: 797AN XY: 727134
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GnomAD4 genome ? AF: 0.0126 AC: 1924AN: 152238Hom.: 39 Cov.: 32 AF XY: 0.0123 AC XY: 917AN XY: 74458
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475
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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
Uncertain
DEOGEN2
Benign
T;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N;.
REVEL
Benign
Sift
Uncertain
D;D;.
Sift4G
Benign
T;T;T
Polyphen
B;B;.
Vest4
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