rs2448020
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_201269.3(ZNF644):c.3791+20A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 1,587,532 control chromosomes in the GnomAD database, including 13,560 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.11 ( 1055 hom., cov: 32)
Exomes 𝑓: 0.13 ( 12505 hom. )
Consequence
ZNF644
NM_201269.3 intron
NM_201269.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.75
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF644 | NM_201269.3 | c.3791+20A>C | intron_variant | ENST00000337393.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF644 | ENST00000337393.10 | c.3791+20A>C | intron_variant | 1 | NM_201269.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.114 AC: 17382AN: 152110Hom.: 1058 Cov.: 32
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GnomAD3 exomes AF: 0.121 AC: 30327AN: 251074Hom.: 2022 AF XY: 0.124 AC XY: 16859AN XY: 135682
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GnomAD4 exome AF: 0.129 AC: 185096AN: 1435306Hom.: 12505 Cov.: 25 AF XY: 0.130 AC XY: 93043AN XY: 715742
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GnomAD4 genome ? AF: 0.114 AC: 17384AN: 152226Hom.: 1055 Cov.: 32 AF XY: 0.113 AC XY: 8430AN XY: 74434
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at