20-5106074-GACAAAC-G
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The ENST00000342308.10(TMEM230):c.411+108_411+113delGTTTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 1,158,510 control chromosomes in the GnomAD database, including 29,580 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.33 ( 6415 hom., cov: 0)
Exomes 𝑓: 0.23 ( 23165 hom. )
Consequence
TMEM230
ENST00000342308.10 intron
ENST00000342308.10 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.315
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 -10 ACMG points.
BP6
Variant 20-5106074-GACAAAC-G is Benign according to our data. Variant chr20-5106074-GACAAAC-G is described in ClinVar as [Benign]. Clinvar id is 1230424.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM230 | NM_001330987.2 | c.222+108_222+113delGTTTGT | intron_variant | NP_001317916.1 | ||||
TMEM230 | NM_001009924.2 | c.222+108_222+113delGTTTGT | intron_variant | NP_001009924.1 | ||||
TMEM230 | NM_001009925.2 | c.222+108_222+113delGTTTGT | intron_variant | NP_001009925.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.330 AC: 41667AN: 126166Hom.: 6411 Cov.: 0
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GnomAD4 exome AF: 0.234 AC: 241118AN: 1032246Hom.: 23165 AF XY: 0.234 AC XY: 119671AN XY: 511404
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GnomAD4 genome AF: 0.330 AC: 41683AN: 126264Hom.: 6415 Cov.: 0 AF XY: 0.330 AC XY: 19981AN XY: 60614
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 16, 2021 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at