rs6116651
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001009923.2(TMEM230):c.306T>A(p.Pro102=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 1,606,410 control chromosomes in the GnomAD database, including 12,030 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.15 ( 2445 hom., cov: 32)
Exomes 𝑓: 0.11 ( 9585 hom. )
Consequence
TMEM230
NM_001009923.2 synonymous
NM_001009923.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.668
Genes affected
TMEM230 (HGNC:15876): (transmembrane protein 230) This gene encodes a multi-pass transmembrane protein that belongs to the TMEM134/TMEM230 protein family. The encoded protein localizes to secretory and recycling vesicle in the neuron and may be involved in synaptic vesicles trafficking and recycling. Mutations in this gene may be linked to familial Parkinson's disease. [provided by RefSeq, Mar 2017]
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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=-0.63).
BP6
?
Variant 20-5106293-A-T is Benign according to our data. Variant chr20-5106293-A-T is described in ClinVar as [Benign]. Clinvar id is 1265859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.668 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM230 | NM_001009923.2 | c.306T>A | p.Pro102= | synonymous_variant | 4/5 | ENST00000342308.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM230 | ENST00000342308.10 | c.306T>A | p.Pro102= | synonymous_variant | 4/5 | 2 | NM_001009923.2 |
Frequencies
GnomAD3 genomes ? AF: 0.152 AC: 23120AN: 152060Hom.: 2441 Cov.: 32
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GnomAD3 exomes AF: 0.0997 AC: 24264AN: 243446Hom.: 1717 AF XY: 0.0964 AC XY: 12697AN XY: 131664
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GnomAD4 exome AF: 0.107 AC: 155483AN: 1454232Hom.: 9585 Cov.: 33 AF XY: 0.105 AC XY: 76158AN XY: 723318
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GnomAD4 genome ? AF: 0.152 AC: 23150AN: 152178Hom.: 2445 Cov.: 32 AF XY: 0.149 AC XY: 11062AN XY: 74410
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 05, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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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