18-75063352-C-T
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_017757.3(ZNF407):c.5631C>T(p.Ala1877=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000281 in 1,460,320 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: 0.000028 ( 0 hom. )
Consequence
ZNF407
NM_017757.3 synonymous
NM_017757.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.956
Genes affected
ZNF407 (HGNC:19904): (zinc finger protein 407) This gene encodes a zinc finger protein whose exact function is not known. It may be involved in transcriptional regulation. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP7
Synonymous conserved (PhyloP=-0.956 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ZNF407 | NM_017757.3 | c.5631C>T | p.Ala1877= | synonymous_variant | 9/9 | ENST00000299687.10 | NP_060227.2 | |
| ZNF407 | NM_001384475.1 | c.5631C>T | p.Ala1877= | synonymous_variant | 9/9 | NP_001371404.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ZNF407 | ENST00000299687.10 | c.5631C>T | p.Ala1877= | synonymous_variant | 9/9 | 1 | NM_017757.3 | ENSP00000299687 | P2 | |
| ZNF407 | ENST00000579200.1 | n.2071C>T | non_coding_transcript_exon_variant | 1/1 | ||||||
| ZNF407 | ENST00000582214.1 | n.349C>T | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.0000123 AC: 3AN: 243742Hom.: 0 AF XY: 0.00000752 AC XY: 1AN XY: 132908
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GnomAD4 exome AF: 0.0000281 AC: 41AN: 1460320Hom.: 0 Cov.: 29 AF XY: 0.0000275 AC XY: 20AN XY: 726428
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GnomAD4 genome
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32
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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 | Genetic Services Laboratory, University of Chicago | Aug 12, 2014 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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