chr8-105419192-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_012082.4(ZFPM2):āc.89A>Gā(p.Glu30Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00419 in 1,613,668 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. E30E) has been classified as Likely benign.
Frequency
Consequence
NM_012082.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZFPM2 | NM_012082.4 | c.89A>G | p.Glu30Gly | missense_variant | 2/8 | ENST00000407775.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFPM2 | ENST00000407775.7 | c.89A>G | p.Glu30Gly | missense_variant | 2/8 | 1 | NM_012082.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00297 AC: 452AN: 152198Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00269 AC: 669AN: 248808Hom.: 4 AF XY: 0.00274 AC XY: 370AN XY: 134990
GnomAD4 exome AF: 0.00432 AC: 6315AN: 1461352Hom.: 16 Cov.: 31 AF XY: 0.00425 AC XY: 3088AN XY: 726950
GnomAD4 genome AF: 0.00297 AC: 452AN: 152316Hom.: 2 Cov.: 32 AF XY: 0.00277 AC XY: 206AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2023 | ZFPM2: BP4, BS1, BS2 - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Diaphragmatic hernia 3 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 2015 | - - |
Double outlet right ventricle Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 2015 | - - |
Tetralogy of Fallot Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 2015 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 08, 2017 | - - |
46,XY sex reversal 9 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 21, 2024 | - - |
46,XY sex reversal 3 Benign:1
Benign, no assertion criteria provided | research | Reproductive Development, Murdoch Childrens Research Institute | Aug 26, 2019 | - - |
ZFPM2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 16, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at