3-43081420-C-T
Position:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6BP7BS1
The NM_032806.6(POMGNT2):c.12G>A(p.Ser4Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 1,571,152 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.000079 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
POMGNT2
NM_032806.6 synonymous
NM_032806.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.06
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 3-43081420-C-T is Benign according to our data. Variant chr3-43081420-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 436368.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Likely_benign=2}.
BP7
Synonymous conserved (PhyloP=-3.06 with no splicing effect.
BS1
Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.000108 (153/1418846) while in subpopulation SAS AF= 0.000672 (53/78874). AF 95% confidence interval is 0.000527. There are 0 homozygotes in gnomad4_exome. There are 89 alleles in male gnomad4_exome subpopulation. Median coverage is 37. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POMGNT2 | NM_032806.6 | c.12G>A | p.Ser4Ser | synonymous_variant | 2/2 | ENST00000344697.3 | NP_116195.2 | |
POMGNT2 | XM_005265515.4 | c.12G>A | p.Ser4Ser | synonymous_variant | 3/3 | XP_005265572.1 | ||
POMGNT2 | XM_011534163.3 | c.12G>A | p.Ser4Ser | synonymous_variant | 3/3 | XP_011532465.1 | ||
POMGNT2 | XM_017007353.2 | c.12G>A | p.Ser4Ser | synonymous_variant | 4/4 | XP_016862842.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152188Hom.: 0 Cov.: 33
GnomAD3 genomes
AF:
AC:
12
AN:
152188
Hom.:
Cov.:
33
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: 0.000176 AC: 36AN: 204806Hom.: 0 AF XY: 0.000190 AC XY: 21AN XY: 110286
GnomAD3 exomes
AF:
AC:
36
AN:
204806
Hom.:
AF XY:
AC XY:
21
AN XY:
110286
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: 0.000108 AC: 153AN: 1418846Hom.: 0 Cov.: 37 AF XY: 0.000127 AC XY: 89AN XY: 701790
GnomAD4 exome
AF:
AC:
153
AN:
1418846
Hom.:
Cov.:
37
AF XY:
AC XY:
89
AN XY:
701790
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: 0.0000788 AC: 12AN: 152306Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74476
GnomAD4 genome
AF:
AC:
12
AN:
152306
Hom.:
Cov.:
33
AF XY:
AC XY:
4
AN XY:
74476
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Bravo
AF:
Asia WGS
AF:
AC:
2
AN:
3478
ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:2
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 25, 2015 | - - |
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 05, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | POMGNT2: BP4, BP7 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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