19-44118191-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_013362.4(ZNF225):c.19G>A(p.Ala7Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,611,466 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_013362.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF225 | NM_013362.4 | c.19G>A | p.Ala7Thr | missense_variant | 3/5 | ENST00000262894.11 | |
ZNF225 | NM_001321685.2 | c.19G>A | p.Ala7Thr | missense_variant | 4/6 | ||
ZNF225 | XM_011527285.3 | c.19G>A | p.Ala7Thr | missense_variant | 3/5 | ||
ZNF225 | XM_011527286.3 | c.19G>A | p.Ala7Thr | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF225 | ENST00000262894.11 | c.19G>A | p.Ala7Thr | missense_variant | 3/5 | 1 | NM_013362.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249450Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 134950
GnomAD4 exome AF: 0.0000288 AC: 42AN: 1459338Hom.: 1 Cov.: 31 AF XY: 0.0000344 AC XY: 25AN XY: 726122
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2022 | The c.19G>A (p.A7T) alteration is located in exon 3 (coding exon 2) of the ZNF225 gene. This alteration results from a G to A substitution at nucleotide position 19, causing the alanine (A) at amino acid position 7 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2023 | ZNF225: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at