16-31914773-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003414.6(ZNF267):c.524T>A(p.Leu175His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000207 in 1,613,602 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_003414.6 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 |
---|---|---|---|---|---|---|---|
ZNF267 | NM_003414.6 | c.524T>A | p.Leu175His | missense_variant | 4/4 | ENST00000300870.15 | |
ZNF267 | NM_001265588.2 | c.428T>A | p.Leu143His | missense_variant | 5/5 | ||
ZNF267 | NR_049749.2 | n.728T>A | non_coding_transcript_exon_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF267 | ENST00000300870.15 | c.524T>A | p.Leu175His | missense_variant | 4/4 | 1 | NM_003414.6 | P1 | |
ZNF267 | ENST00000575471.2 | n.2920T>A | non_coding_transcript_exon_variant | 1/1 | |||||
ZNF267 | ENST00000394846.7 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152256Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000300 AC: 75AN: 250378Hom.: 0 AF XY: 0.000347 AC XY: 47AN XY: 135374
GnomAD4 exome AF: 0.000211 AC: 309AN: 1461346Hom.: 0 Cov.: 31 AF XY: 0.000248 AC XY: 180AN XY: 726928
GnomAD4 genome AF: 0.000164 AC: 25AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74392
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 08, 2024 | The c.524T>A (p.L175H) alteration is located in exon 4 (coding exon 4) of the ZNF267 gene. This alteration results from a T to A substitution at nucleotide position 524, causing the leucine (L) at amino acid position 175 to be replaced by a histidine (H). 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