chr18-74633794-G-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_017757.3(ZNF407):c.2775G>T(p.Gly925=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000162 in 1,613,798 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00014 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00016 ( 1 hom. )
Consequence
ZNF407
NM_017757.3 synonymous
NM_017757.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.150
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 Benign. Variant got -11 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 18-74633794-G-T is Benign according to our data. Variant chr18-74633794-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 212661.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.15 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF407 | NM_017757.3 | c.2775G>T | p.Gly925= | synonymous_variant | 2/9 | ENST00000299687.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF407 | ENST00000299687.10 | c.2775G>T | p.Gly925= | synonymous_variant | 2/9 | 1 | NM_017757.3 | P2 | |
ZNF407 | ENST00000577538.5 | c.2775G>T | p.Gly925= | synonymous_variant | 1/7 | 2 | A2 | ||
ZNF407 | ENST00000309902.10 | c.2775G>T | p.Gly925= | synonymous_variant | 1/4 | 2 | |||
ZNF407 | ENST00000582337.5 | c.2775G>T | p.Gly925= | synonymous_variant | 2/5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152116Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000144 AC: 36AN: 249186Hom.: 0 AF XY: 0.000141 AC XY: 19AN XY: 135194
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GnomAD4 exome AF: 0.000164 AC: 240AN: 1461682Hom.: 1 Cov.: 44 AF XY: 0.000169 AC XY: 123AN XY: 727124
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GnomAD4 genome AF: 0.000138 AC: 21AN: 152116Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74292
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 23, 2015 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 14, 2018 | - - |
Computational scores
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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