20-5106074-GACAAACAC-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000342308.10(TMEM230):c.411+106_411+113del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 1,158,486 control chromosomes in the GnomAD database, including 5,444 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.10 (885 hom., cov: 0)
  • Exomes 𝑓: 0.12 (4559 hom.)
• Consequence: TMEM230 ENST00000342308.10 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 20-5106074-GACAAACAC-G is Benign according to our data. Variant chr20-5106074-GACAAACAC-G is described in ClinVar as [Benign]. Clinvar id is 1245471.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM230	NM_001009923.2	c.411+106_411+113del		intron_variant		ENST00000342308.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM230	ENST00000342308.10	c.411+106_411+113del		intron_variant		2	NM_001009923.2

Frequencies

GnomAD3 genomes AF: 0.103 AC: 13041 AN: 126342 Hom.: 885 Cov.: 0

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.0192

Gnomad AMR AF: 0.0656

Gnomad ASJ AF: 0.0670

Gnomad EAS AF: 0.0274

Gnomad SAS AF: 0.0820

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0664

Gnomad NFE AF: 0.0705

Gnomad OTH AF: 0.0921

GnomAD4 exome AF: 0.115 AC: 118981 AN: 1032050 Hom.: 4559 AF XY: 0.118 AC XY: 60508 AN XY: 511124

Gnomad4 AFR exome AF: 0.165

Gnomad4 AMR exome AF: 0.0730

Gnomad4 ASJ exome AF: 0.147

Gnomad4 EAS exome AF: 0.106

Gnomad4 SAS exome AF: 0.177

Gnomad4 FIN exome AF: 0.106

Gnomad4 NFE exome AF: 0.111

Gnomad4 OTH exome AF: 0.118

GnomAD4 genome AF: 0.103 AC: 13048 AN: 126436 Hom.: 885 Cov.: 0 AF XY: 0.105 AC XY: 6388 AN XY: 60694

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.0654

Gnomad4 ASJ AF: 0.0670

Gnomad4 EAS AF: 0.0272

Gnomad4 SAS AF: 0.0812

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.0704

Gnomad4 OTH AF: 0.0916

Alfa AF: 0.0817 Hom.: 7

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 19, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs536207512; hg19: chr20-5086720;