8-105318866-G-GGCGGCGGGA

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_012082.4(ZFPM2):​c.-73_-65dupGGCGGGAGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.84 ( 51088 hom., cov: 0)
Exomes 𝑓: 0.76 ( 187936 hom. )

Consequence

ZFPM2
NM_012082.4 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.37

Publications

1 publications found
Variant links:
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]
ZFPM2 Gene-Disease associations (from GenCC):
  • 46,XY sex reversal 9
    Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
  • diaphragmatic hernia 3
    Inheritance: AD Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P
  • tetralogy of fallot
    Inheritance: Unknown, AD Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
  • 46,XY partial gonadal dysgenesis
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6
Variant 8-105318866-G-GGCGGCGGGA is Benign according to our data. Variant chr8-105318866-G-GGCGGCGGGA is described in ClinVar as [Benign]. Clinvar id is 1233669.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZFPM2NM_012082.4 linkc.-73_-65dupGGCGGGAGC 5_prime_UTR_variant Exon 1 of 8 ENST00000407775.7 NP_036214.2 Q8WW38-1Q9NPQ0
ZFPM2NM_001362836.2 linkc.-73_-65dupGGCGGGAGC 5_prime_UTR_variant Exon 1 of 7 NP_001349765.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZFPM2ENST00000407775.7 linkc.-73_-65dupGGCGGGAGC 5_prime_UTR_variant Exon 1 of 8 1 NM_012082.4 ENSP00000384179.2 Q8WW38-1
ZFPM2ENST00000518180.1 linkn.479+72340_479+72348dupGGCGGGAGC intron_variant Intron 4 of 4 4

Frequencies

GnomAD3 genomes
AF:
0.836
AC:
121884
AN:
145846
Hom.:
51051
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.824
Gnomad AMI
AF:
0.877
Gnomad AMR
AF:
0.873
Gnomad ASJ
AF:
0.844
Gnomad EAS
AF:
0.947
Gnomad SAS
AF:
0.880
Gnomad FIN
AF:
0.888
Gnomad MID
AF:
0.876
Gnomad NFE
AF:
0.815
Gnomad OTH
AF:
0.849
GnomAD4 exome
AF:
0.755
AC:
506434
AN:
670558
Hom.:
187936
Cov.:
13
AF XY:
0.754
AC XY:
237842
AN XY:
315646
show subpopulations
African (AFR)
AF:
0.787
AC:
8811
AN:
11192
American (AMR)
AF:
0.784
AC:
806
AN:
1028
Ashkenazi Jewish (ASJ)
AF:
0.784
AC:
3327
AN:
4246
East Asian (EAS)
AF:
0.869
AC:
3109
AN:
3578
South Asian (SAS)
AF:
0.798
AC:
10993
AN:
13784
European-Finnish (FIN)
AF:
0.824
AC:
5929
AN:
7194
Middle Eastern (MID)
AF:
0.825
AC:
1086
AN:
1316
European-Non Finnish (NFE)
AF:
0.751
AC:
455588
AN:
606480
Other (OTH)
AF:
0.772
AC:
16785
AN:
21740
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.559
Heterozygous variant carriers
0
4005
8011
12016
16022
20027
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
15010
30020
45030
60040
75050
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.836
AC:
121967
AN:
145942
Hom.:
51088
Cov.:
0
AF XY:
0.841
AC XY:
59679
AN XY:
70954
show subpopulations
African (AFR)
AF:
0.824
AC:
33578
AN:
40766
American (AMR)
AF:
0.873
AC:
12868
AN:
14740
Ashkenazi Jewish (ASJ)
AF:
0.844
AC:
2855
AN:
3382
East Asian (EAS)
AF:
0.946
AC:
4554
AN:
4812
South Asian (SAS)
AF:
0.881
AC:
4215
AN:
4786
European-Finnish (FIN)
AF:
0.888
AC:
7599
AN:
8558
Middle Eastern (MID)
AF:
0.870
AC:
247
AN:
284
European-Non Finnish (NFE)
AF:
0.815
AC:
53532
AN:
65674
Other (OTH)
AF:
0.848
AC:
1726
AN:
2036
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
983
1966
2950
3933
4916
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
846
1692
2538
3384
4230
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.703
Hom.:
1334

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Jun 19, 2021
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
3.4
Mutation Taster
=299/1
polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs71305140; hg19: chr8-106331094; API