19-12186877-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003437.5(ZNF136):c.499C>T(p.Leu167Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,613,944 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003437.5 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 |
---|---|---|---|---|---|---|---|
ZNF136 | NM_003437.5 | c.499C>T | p.Leu167Phe | missense_variant | 4/4 | ENST00000343979.6 | |
ZNF136 | NM_001348014.2 | c.403C>T | p.Leu135Phe | missense_variant | 5/5 | ||
ZNF136 | NM_001348013.2 | c.301C>T | p.Leu101Phe | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF136 | ENST00000343979.6 | c.499C>T | p.Leu167Phe | missense_variant | 4/4 | 1 | NM_003437.5 | P1 | |
ZNF136 | ENST00000464860.1 | n.1663C>T | non_coding_transcript_exon_variant | 3/3 | 1 | ||||
ZNF136 | ENST00000652580.1 | c.403C>T | p.Leu135Phe | missense_variant | 5/5 | ||||
ZNF136 | ENST00000439995.5 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250938Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135624
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461746Hom.: 1 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 727152
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2023 | The c.499C>T (p.L167F) alteration is located in exon 4 (coding exon 4) of the ZNF136 gene. This alteration results from a C to T substitution at nucleotide position 499, causing the leucine (L) at amino acid position 167 to be replaced by a phenylalanine (F). 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