9-127428858-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.43C>T(p.Pro15Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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.43C>T | p.Pro15Ser | missense_variant | Exon 2 of 5 | 1 | NM_007135.3 | ENSP00000362446.4 | ||
ZNF79 | ENST00000543471 | c.-30C>T | 5_prime_UTR_variant | Exon 3 of 6 | 2 | ENSP00000438418.1 | ||||
ZNF79 | ENST00000612342 | c.-30C>T | 5_prime_UTR_variant | Exon 2 of 5 | 2 | ENSP00000478201.1 | ||||
ZNF79 | ENST00000617266 | c.-137C>T | 5_prime_UTR_variant | Exon 2 of 3 | 3 | ENSP00000484833.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 29
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.43C>T (p.P15S) alteration is located in exon 2 (coding exon 2) of the ZNF79 gene. This alteration results from a C to T substitution at nucleotide position 43, causing the proline (P) at amino acid position 15 to be replaced by a serine (S). 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
Publications
No publications associated with this variant yet.