rs34940122
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_017757.3(ZNF407):āc.5085C>Gā(p.Gly1695=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000225 in 1,556,914 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 Likely benign (ā ).
Frequency
Genomes: š 0.000013 ( 0 hom., cov: 33)
Exomes š: 0.000023 ( 0 hom. )
Consequence
ZNF407
NM_017757.3 synonymous
NM_017757.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.265
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=-0.37).
BP6
?
Variant 18-74881076-C-G is Benign according to our data. Variant chr18-74881076-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 212672.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.265 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF407 | NM_017757.3 | c.5085C>G | p.Gly1695= | synonymous_variant | 6/9 | ENST00000299687.10 | |
ZNF407 | NM_001384475.1 | c.5085C>G | p.Gly1695= | synonymous_variant | 6/9 | ||
ZNF407 | NM_001146189.1 | c.5085C>G | p.Gly1695= | synonymous_variant | 5/7 | ||
ZNF407 | XM_017025838.3 | c.5085C>G | p.Gly1695= | synonymous_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF407 | ENST00000299687.10 | c.5085C>G | p.Gly1695= | synonymous_variant | 6/9 | 1 | NM_017757.3 | P2 | |
ZNF407 | ENST00000577538.5 | c.5085C>G | p.Gly1695= | synonymous_variant | 5/7 | 2 | A2 | ||
ZNF407 | ENST00000581829.2 | c.201C>G | p.Gly67= | synonymous_variant | 2/4 | 5 | |||
ZNF407 | ENST00000584235.5 | c.207C>G | p.Gly69= | synonymous_variant | 2/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152014Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000300 AC: 49AN: 163360Hom.: 0 AF XY: 0.000261 AC XY: 23AN XY: 87996
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GnomAD4 exome AF: 0.0000235 AC: 33AN: 1404900Hom.: 0 Cov.: 31 AF XY: 0.0000274 AC XY: 19AN XY: 694472
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GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152014Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74248
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
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 | - - |
Computational scores
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Name
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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