19-44130967-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_013362.4(ZNF225):c.353T>C(p.Met118Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 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_013362.4 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 |
---|---|---|---|---|---|---|---|
ZNF225 | NM_013362.4 | c.353T>C | p.Met118Thr | missense_variant | 5/5 | ENST00000262894.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF225 | ENST00000262894.11 | c.353T>C | p.Met118Thr | missense_variant | 5/5 | 1 | NM_013362.4 | P1 | |
ZNF225 | ENST00000590612.1 | c.353T>C | p.Met118Thr | missense_variant | 4/4 | 1 | P1 | ||
ZNF225 | ENST00000589155.5 | c.353T>C | p.Met118Thr | missense_variant | 5/5 | 4 | |||
ZNF225 | ENST00000592780.5 | c.*134T>C | 3_prime_UTR_variant | 6/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249776Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135484
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461794Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727182
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2021 | The c.353T>C (p.M118T) alteration is located in exon 5 (coding exon 4) of the ZNF225 gene. This alteration results from a T to C substitution at nucleotide position 353, causing the methionine (M) at amino acid position 118 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