chr19-44131549-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_013362.4(ZNF225):c.935G>A(p.Arg312Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000171 in 1,614,190 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 Likely benign (★★).
Frequency
Consequence
NM_013362.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF225 | NM_013362.4 | c.935G>A | p.Arg312Gln | missense_variant | 5/5 | ENST00000262894.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF225 | ENST00000262894.11 | c.935G>A | p.Arg312Gln | missense_variant | 5/5 | 1 | NM_013362.4 | P1 | |
ZNF225 | ENST00000590612.1 | c.935G>A | p.Arg312Gln | missense_variant | 4/4 | 1 | P1 | ||
ZNF225 | ENST00000592780.5 | c.*716G>A | 3_prime_UTR_variant | 6/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000250 AC: 38AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000339 AC: 85AN: 250564Hom.: 0 AF XY: 0.000287 AC XY: 39AN XY: 135772
GnomAD4 exome AF: 0.000163 AC: 238AN: 1461850Hom.: 1 Cov.: 32 AF XY: 0.000169 AC XY: 123AN XY: 727222
GnomAD4 genome ? AF: 0.000249 AC: 38AN: 152340Hom.: 0 Cov.: 33 AF XY: 0.000201 AC XY: 15AN XY: 74484
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | ZNF225: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at