rs370159868
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017757.3(ZNF407):āc.6734T>Cā(p.Leu2245Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000121 in 1,490,584 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ).
Frequency
Consequence
NM_017757.3 missense
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 | UniProt |
---|---|---|---|---|---|---|---|
ZNF407 | NM_017757.3 | c.6734T>C | p.Leu2245Pro | missense_variant | 9/9 | ENST00000299687.10 | |
ZNF407 | NM_001384475.1 | c.6734T>C | p.Leu2245Pro | missense_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF407 | ENST00000299687.10 | c.6734T>C | p.Leu2245Pro | missense_variant | 9/9 | 1 | NM_017757.3 | P2 | |
ZNF407 | ENST00000579200.1 | n.3174T>C | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152140Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000897 AC: 12AN: 1338326Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 9AN XY: 653146
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74440
ClinVar
Submissions by phenotype
not specified Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | The c.6734T>C (p.L2245P) alteration is located in exon 8 (coding exon 8) of the ZNF407 gene. This alteration results from a T to C substitution at nucleotide position 6734, causing the leucine (L) at amino acid position 2245 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 17, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at