rs187003222
Positions:
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_032806.6(POMGNT2):c.861G>A(p.Glu287=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000471 in 1,614,238 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000047 ( 0 hom. )
Consequence
POMGNT2
NM_032806.6 synonymous
NM_032806.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.15
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
?
Variant 3-43080571-C-T is Benign according to our data. Variant chr3-43080571-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 540498.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.14 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0000525 (8/152362) while in subpopulation EAS AF= 0.00154 (8/5186). AF 95% confidence interval is 0.000767. There are 0 homozygotes in gnomad4. There are 6 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POMGNT2 | NM_032806.6 | c.861G>A | p.Glu287= | synonymous_variant | 2/2 | ENST00000344697.3 | |
POMGNT2 | XM_005265515.4 | c.861G>A | p.Glu287= | synonymous_variant | 3/3 | ||
POMGNT2 | XM_011534163.3 | c.861G>A | p.Glu287= | synonymous_variant | 3/3 | ||
POMGNT2 | XM_017007353.2 | c.861G>A | p.Glu287= | synonymous_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POMGNT2 | ENST00000344697.3 | c.861G>A | p.Glu287= | synonymous_variant | 2/2 | 1 | NM_032806.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000525 AC: 8AN: 152244Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251352Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135842
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GnomAD4 exome AF: 0.0000465 AC: 68AN: 1461876Hom.: 0 Cov.: 37 AF XY: 0.0000536 AC XY: 39AN XY: 727240
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GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152362Hom.: 0 Cov.: 33 AF XY: 0.0000805 AC XY: 6AN XY: 74502
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 8 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2018 | - - |
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