rs201719725
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_017757.3(ZNF407):c.4278G>A(p.Leu1426=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00339 in 1,614,024 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0021 ( 1 hom., cov: 33)
Exomes 𝑓: 0.0035 ( 11 hom. )
Consequence
ZNF407
NM_017757.3 synonymous
NM_017757.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.98
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
?
Variant 18-74635297-G-A is Benign according to our data. Variant chr18-74635297-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 212670.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=1.98 with no splicing effect.
BS2
?
High Homozygotes in GnomAdExome4 at 11 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF407 | NM_017757.3 | c.4278G>A | p.Leu1426= | synonymous_variant | 2/9 | ENST00000299687.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF407 | ENST00000299687.10 | c.4278G>A | p.Leu1426= | synonymous_variant | 2/9 | 1 | NM_017757.3 | P2 | |
ZNF407 | ENST00000577538.5 | c.4278G>A | p.Leu1426= | synonymous_variant | 1/7 | 2 | A2 | ||
ZNF407 | ENST00000309902.10 | c.4278G>A | p.Leu1426= | synonymous_variant | 1/4 | 2 | |||
ZNF407 | ENST00000582337.5 | c.4278G>A | p.Leu1426= | synonymous_variant | 2/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00214 AC: 326AN: 152206Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00223 AC: 555AN: 249166Hom.: 0 AF XY: 0.00202 AC XY: 273AN XY: 135184
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GnomAD4 exome AF: 0.00352 AC: 5150AN: 1461700Hom.: 11 Cov.: 41 AF XY: 0.00334 AC XY: 2431AN XY: 727130
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GnomAD4 genome ? AF: 0.00214 AC: 326AN: 152324Hom.: 1 Cov.: 33 AF XY: 0.00200 AC XY: 149AN XY: 74496
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ClinVar
Significance: Benign/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 | Aug 01, 2018 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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