chr19-44131876-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_013362.4(ZNF225):c.1262C>T(p.Ala421Val) 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 1,613,552 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A421G) has been classified 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.1262C>T | p.Ala421Val | missense_variant | 5/5 | ENST00000262894.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF225 | ENST00000262894.11 | c.1262C>T | p.Ala421Val | missense_variant | 5/5 | 1 | NM_013362.4 | P1 | |
ZNF225 | ENST00000590612.1 | c.1262C>T | p.Ala421Val | missense_variant | 4/4 | 1 | P1 | ||
ZNF225 | ENST00000592780.5 | c.*1043C>T | 3_prime_UTR_variant | 6/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000659 AC: 1AN: 151666Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250690Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135782
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461886Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727242
GnomAD4 genome ? AF: 0.00000659 AC: 1AN: 151666Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74050
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 30, 2023 | The c.1262C>T (p.A421V) alteration is located in exon 5 (coding exon 4) of the ZNF225 gene. This alteration results from a C to T substitution at nucleotide position 1262, causing the alanine (A) at amino acid position 421 to be replaced by a valine (V). 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