rs183815209
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6BP7
The ENST00000299687.10(ZNF407):c.5589G>A(p.Val1863=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000239 in 1,613,664 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
ENST00000299687.10 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF407 | NM_017757.3 | c.5589G>A | p.Val1863= | synonymous_variant | 9/9 | ENST00000299687.10 | NP_060227.2 | |
ZNF407 | NM_001384475.1 | c.5589G>A | p.Val1863= | synonymous_variant | 9/9 | NP_001371404.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF407 | ENST00000299687.10 | c.5589G>A | p.Val1863= | synonymous_variant | 9/9 | 1 | NM_017757.3 | ENSP00000299687 | P2 | |
ZNF407 | ENST00000579200.1 | n.2029G>A | non_coding_transcript_exon_variant | 1/1 | ||||||
ZNF407 | ENST00000582214.1 | n.307G>A | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00118 AC: 180AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000317 AC: 78AN: 246336Hom.: 0 AF XY: 0.000239 AC XY: 32AN XY: 133928
GnomAD4 exome AF: 0.000142 AC: 208AN: 1461356Hom.: 0 Cov.: 29 AF XY: 0.000120 AC XY: 87AN XY: 726962
GnomAD4 genome AF: 0.00117 AC: 178AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.00118 AC XY: 88AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 12, 2015 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 05, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at