9-127435995-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007135.3(ZNF79):c.320C>T(p.Pro107Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,613,926 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007135.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF79 | ENST00000342483.5 | c.320C>T | p.Pro107Leu | missense_variant | Exon 4 of 5 | 1 | NM_007135.3 | ENSP00000362446.4 | ||
ZNF79 | ENST00000543471.5 | c.248C>T | p.Pro83Leu | missense_variant | Exon 5 of 6 | 2 | ENSP00000438418.1 | |||
ZNF79 | ENST00000612342.4 | c.248C>T | p.Pro83Leu | missense_variant | Exon 4 of 5 | 2 | ENSP00000478201.1 | |||
ZNF79 | ENST00000617266.2 | c.-75+7075C>T | intron_variant | Intron 2 of 2 | 3 | ENSP00000484833.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152196Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251404Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135876
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461730Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727162
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152196Hom.: 0 Cov.: 34 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.320C>T (p.P107L) alteration is located in exon 4 (coding exon 4) of the ZNF79 gene. This alteration results from a C to T substitution at nucleotide position 320, causing the proline (P) at amino acid position 107 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at