rs920628
Positions:
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_012082.4(ZFPM2):āc.1362A>Gā(p.Pro454=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0406 in 1,613,784 control chromosomes in the GnomAD database, including 5,110 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.11 ( 2406 hom., cov: 32)
Exomes š: 0.033 ( 2704 hom. )
Consequence
ZFPM2
NM_012082.4 synonymous
NM_012082.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.167
Genes affected
ZFPM2 (HGNC:16700): (zinc finger protein, FOG family member 2) The zinc finger protein encoded by this gene is a widely expressed member of the FOG family of transcription factors. The family members modulate the activity of GATA family proteins, which are important regulators of hematopoiesis and cardiogenesis in mammals. It has been demonstrated that the protein can both activate and down-regulate expression of GATA-target genes, suggesting different modulation in different promoter contexts. A related mRNA suggests an alternatively spliced product but this information is not yet fully supported by the sequence. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BP6
?
Variant 8-105801444-A-G is Benign according to our data. Variant chr8-105801444-A-G is described in ClinVar as [Benign]. Clinvar id is 260171.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-105801444-A-G is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.167 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZFPM2 | NM_012082.4 | c.1362A>G | p.Pro454= | synonymous_variant | 8/8 | ENST00000407775.7 | |
ZFPM2-AS1 | NR_125797.1 | n.191-3002T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFPM2 | ENST00000407775.7 | c.1362A>G | p.Pro454= | synonymous_variant | 8/8 | 1 | NM_012082.4 | P1 | |
ZFPM2-AS1 | ENST00000520433.5 | n.212-3002T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.112 AC: 17092AN: 152026Hom.: 2387 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
17092
AN:
152026
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0462 AC: 11487AN: 248804Hom.: 1058 AF XY: 0.0406 AC XY: 5483AN XY: 134998
GnomAD3 exomes
AF:
AC:
11487
AN:
248804
Hom.:
AF XY:
AC XY:
5483
AN XY:
134998
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0331 AC: 48333AN: 1461640Hom.: 2704 Cov.: 31 AF XY: 0.0319 AC XY: 23197AN XY: 727102
GnomAD4 exome
AF:
AC:
48333
AN:
1461640
Hom.:
Cov.:
31
AF XY:
AC XY:
23197
AN XY:
727102
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.113 AC: 17156AN: 152144Hom.: 2406 Cov.: 32 AF XY: 0.109 AC XY: 8093AN XY: 74398
GnomAD4 genome
?
AF:
AC:
17156
AN:
152144
Hom.:
Cov.:
32
AF XY:
AC XY:
8093
AN XY:
74398
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
234
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Apr 10, 2023 | - - |
46,XY sex reversal 9 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 17, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at