19-12187097-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003437.5(ZNF136):c.719G>A(p.Arg240Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,613,952 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_003437.5 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 |
---|---|---|---|---|---|---|---|
ZNF136 | NM_003437.5 | c.719G>A | p.Arg240Gln | missense_variant | 4/4 | ENST00000343979.6 | |
ZNF136 | NM_001348014.2 | c.623G>A | p.Arg208Gln | missense_variant | 5/5 | ||
ZNF136 | NM_001348013.2 | c.521G>A | p.Arg174Gln | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF136 | ENST00000343979.6 | c.719G>A | p.Arg240Gln | missense_variant | 4/4 | 1 | NM_003437.5 | P1 | |
ZNF136 | ENST00000464860.1 | n.1883G>A | non_coding_transcript_exon_variant | 3/3 | 1 | ||||
ZNF136 | ENST00000652580.1 | c.623G>A | p.Arg208Gln | missense_variant | 5/5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251322Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135834
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461838Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 727210
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 06, 2023 | The c.719G>A (p.R240Q) alteration is located in exon 4 (coding exon 4) of the ZNF136 gene. This alteration results from a G to A substitution at nucleotide position 719, causing the arginine (R) at amino acid position 240 to be replaced by a glutamine (Q). 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