16-31885179-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003414.6(ZNF267):c.149C>T(p.Pro50Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000286 in 1,610,850 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003414.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF267 | NM_003414.6 | c.149C>T | p.Pro50Leu | missense_variant | 3/4 | ENST00000300870.15 | |
ZNF267 | NM_001265588.2 | c.53C>T | p.Pro18Leu | missense_variant | 4/5 | ||
ZNF267 | NR_049749.2 | n.309C>T | non_coding_transcript_exon_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF267 | ENST00000300870.15 | c.149C>T | p.Pro50Leu | missense_variant | 3/4 | 1 | NM_003414.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152102Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251016Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135692
GnomAD4 exome AF: 0.0000288 AC: 42AN: 1458748Hom.: 0 Cov.: 30 AF XY: 0.0000276 AC XY: 20AN XY: 725706
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152102Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74286
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 13, 2023 | The c.149C>T (p.P50L) alteration is located in exon 3 (coding exon 3) of the ZNF267 gene. This alteration results from a C to T substitution at nucleotide position 149, causing the proline (P) at amino acid position 50 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