20-5106074-GACAAAC-G

Variant summary

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

The ENST00000342308.10(TMEM230):c.411+108_411+113del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 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
• 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-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	UniProt
TMEM230	NM_001009923.2	c.411+108_411+113del		intron_variant		ENST00000342308.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM230	ENST00000342308.10	c.411+108_411+113del		intron_variant		2	NM_001009923.2

Frequencies

GnomAD3 genomes AF: 0.330 AC: 41667 AN: 126166 Hom.: 6411 Cov.: 0

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.336

GnomAD4 exome AF: 0.234 AC: 241118 AN: 1032246 Hom.: 23165 AF XY: 0.234 AC XY: 119671 AN XY: 511404

Gnomad4 AFR exome AF: 0.128

Gnomad4 AMR exome AF: 0.121

Gnomad4 ASJ exome AF: 0.273

Gnomad4 EAS exome AF: 0.181

Gnomad4 SAS exome AF: 0.293

Gnomad4 FIN exome AF: 0.168

Gnomad4 NFE exome AF: 0.239

Gnomad4 OTH exome AF: 0.232

GnomAD4 genome AF: 0.330 AC: 41683 AN: 126264 Hom.: 6415 Cov.: 0 AF XY: 0.330 AC XY: 19981 AN XY: 60614

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.342

Alfa AF: 0.261 Hom.: 23

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 16, 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: rs150372292; hg19: chr20-5086720;