rs35207939
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_032806.6(POMGNT2):c.1488C>T(p.Gly496=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0143 in 1,613,972 control chromosomes in the GnomAD database, including 208 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0096 ( 11 hom., cov: 33)
Exomes 𝑓: 0.015 ( 197 hom. )
Consequence
POMGNT2
NM_032806.6 synonymous
NM_032806.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.789
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 3-43079944-G-A is Benign according to our data. Variant chr3-43079944-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 262105.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-43079944-G-A is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.789 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00965 (1470/152334) while in subpopulation NFE AF= 0.0156 (1063/68030). AF 95% confidence interval is 0.0148. There are 11 homozygotes in gnomad4. There are 681 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 11 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POMGNT2 | NM_032806.6 | c.1488C>T | p.Gly496= | synonymous_variant | 2/2 | ENST00000344697.3 | |
POMGNT2 | XM_005265515.4 | c.1488C>T | p.Gly496= | synonymous_variant | 3/3 | ||
POMGNT2 | XM_011534163.3 | c.1488C>T | p.Gly496= | synonymous_variant | 3/3 | ||
POMGNT2 | XM_017007353.2 | c.1488C>T | p.Gly496= | synonymous_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POMGNT2 | ENST00000344697.3 | c.1488C>T | p.Gly496= | synonymous_variant | 2/2 | 1 | NM_032806.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00966 AC: 1470AN: 152216Hom.: 11 Cov.: 33
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GnomAD3 exomes AF: 0.0103 AC: 2573AN: 250656Hom.: 19 AF XY: 0.0102 AC XY: 1383AN XY: 135556
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GnomAD4 exome AF: 0.0148 AC: 21681AN: 1461638Hom.: 197 Cov.: 29 AF XY: 0.0144 AC XY: 10451AN XY: 727134
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:5
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 | GeneDx | Sep 19, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jul 31, 2019 | - - |
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8;C4748320:Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 8 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jul 08, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at