20-5106076-CAA-C

Variant summary

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

The ENST00000342308.10(TMEM230):c.411+110_411+111del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 409,770 control chromosomes in the GnomAD database, including 5,301 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.26 (481 hom., cov: 0)
  • Exomes 𝑓: 0.15 (4820 hom.)
• Consequence: TMEM230 ENST00000342308.10 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.895

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 20-5106076-CAA-C is Benign according to our data. Variant chr20-5106076-CAA-C is described in ClinVar as [Benign]. Clinvar id is 1182099.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM230	NM_001009923.2	c.411+110_411+111del		intron_variant		ENST00000342308.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM230	ENST00000342308.10	c.411+110_411+111del		intron_variant		2	NM_001009923.2

Frequencies

GnomAD3 genomes AF: 0.263 AC: 10872 AN: 41400 Hom.: 478 Cov.: 0

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.0228

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.333

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.295

GnomAD4 exome AF: 0.146 AC: 53889 AN: 368322 Hom.: 4820 AF XY: 0.149 AC XY: 26839 AN XY: 180564

Gnomad4 AFR exome AF: 0.338

Gnomad4 AMR exome AF: 0.0928

Gnomad4 ASJ exome AF: 0.236

Gnomad4 EAS exome AF: 0.0121

Gnomad4 SAS exome AF: 0.251

Gnomad4 FIN exome AF: 0.0846

Gnomad4 NFE exome AF: 0.148

Gnomad4 OTH exome AF: 0.165

GnomAD4 genome AF: 0.263 AC: 10893 AN: 41448 Hom.: 481 Cov.: 0 AF XY: 0.262 AC XY: 5180 AN XY: 19766

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.0235

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.294

Alfa AF: 0.0703 Hom.: 0

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

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs71868595; hg19: chr20-5086722;