16-3437398-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000301744.7(ZNF597):c.301C>A(p.Pro101Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000106 in 1,614,006 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
ENST00000301744.7 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF597 | NM_152457.3 | c.301C>A | p.Pro101Thr | missense_variant | 4/4 | ENST00000301744.7 | NP_689670.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF597 | ENST00000301744.7 | c.301C>A | p.Pro101Thr | missense_variant | 4/4 | 1 | NM_152457.3 | ENSP00000301744 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000336 AC: 51AN: 151998Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000875 AC: 22AN: 251484Hom.: 0 AF XY: 0.0000809 AC XY: 11AN XY: 135918
GnomAD4 exome AF: 0.0000787 AC: 115AN: 1461890Hom.: 0 Cov.: 32 AF XY: 0.0000866 AC XY: 63AN XY: 727246
GnomAD4 genome AF: 0.000368 AC: 56AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.000430 AC XY: 32AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 21, 2021 | The c.301C>A (p.P101T) alteration is located in exon 4 (coding exon 3) of the ZNF597 gene. This alteration results from a C to A substitution at nucleotide position 301, causing the proline (P) at amino acid position 101 to be replaced by a threonine (T). 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