20-5106074-GACAAACACAC-G

Variant summary

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

The ENST00000342308.10(TMEM230):c.411+104_411+113del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.044 in 1,163,048 control chromosomes in the GnomAD database, including 2,543 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.10 (1574 hom., cov: 0)
  • Exomes 𝑓: 0.037 (969 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-GACAAACACAC-G is Benign according to our data. Variant chr20-5106074-GACAAACACAC-G is described in ClinVar as [Benign]. Clinvar id is 1288935.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM230	NM_001009923.2	c.411+104_411+113del		intron_variant		ENST00000342308.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM230	ENST00000342308.10	c.411+104_411+113del		intron_variant		2	NM_001009923.2

Frequencies

GnomAD3 genomes AF: 0.101 AC: 12740 AN: 126394 Hom.: 1572 Cov.: 0

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0661

Gnomad ASJ AF: 0.0336

Gnomad EAS AF: 0.0243

Gnomad SAS AF: 0.0118

Gnomad FIN AF: 0.00434

Gnomad MID AF: 0.0833

Gnomad NFE AF: 0.0164

Gnomad OTH AF: 0.0868

GnomAD4 exome AF: 0.0370 AC: 38367 AN: 1036560 Hom.: 969 AF XY: 0.0376 AC XY: 19309 AN XY: 513544

Gnomad4 AFR exome AF: 0.248

Gnomad4 AMR exome AF: 0.0440

Gnomad4 ASJ exome AF: 0.0532

Gnomad4 EAS exome AF: 0.0341

Gnomad4 SAS exome AF: 0.0490

Gnomad4 FIN exome AF: 0.0298

Gnomad4 NFE exome AF: 0.0297

Gnomad4 OTH exome AF: 0.0489

GnomAD4 genome AF: 0.101 AC: 12763 AN: 126488 Hom.: 1574 Cov.: 0 AF XY: 0.0996 AC XY: 6047 AN XY: 60728

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.0660

Gnomad4 ASJ AF: 0.0336

Gnomad4 EAS AF: 0.0244

Gnomad4 SAS AF: 0.0123

Gnomad4 FIN AF: 0.00434

Gnomad4 NFE AF: 0.0164

Gnomad4 OTH AF: 0.0864

Alfa AF: 0.0728 Hom.: 18

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 21, 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: rs71197751; hg19: chr20-5086720;