Variant 20-5106078-A-AACAC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000342308.10(TMEM230):c.411+109_411+110insGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0449 in 544,376 control chromosomes in the GnomAD database, including 255 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.081 ( 191 hom., cov: 0)

Exomes 𝑓: 0.039 ( 64 hom. )

Consequence

TMEM230
ENST00000342308.10 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.315

Variant links:

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]

TMEM230 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 20-5106078-A-AACAC is Benign according to our data. Variant chr20-5106078-A-AACAC is described in ClinVar as [Benign]. Clinvar id is 1265588.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM230	NM_001009923.2 linkuse as main transcript	c.411+109_411+110insGTGT		intron_variant		ENST00000342308.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM230	ENST00000342308.10 linkuse as main transcript	c.411+109_411+110insGTGT		intron_variant		2	NM_001009923.2		Q96A57-2

Frequencies

GnomAD3 genomes

AF:

0.0808

AC:

6284

AN:

77802

Hom.:

192

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0473

Gnomad AMI

AF:

0.225

Gnomad AMR

AF:

0.0845

Gnomad ASJ

AF:

0.0468

Gnomad EAS

AF:

0.102

Gnomad SAS

AF:

0.0324

Gnomad FIN

AF:

0.118

Gnomad MID

AF:

0.0833

Gnomad NFE

AF:

0.0835

Gnomad OTH

AF:

0.0768

GnomAD4 exome

AF:

0.0389

AC:

18158

AN:

466548

Hom.:

AF XY:

0.0393

AC XY:

8983

AN XY:

228520

show subpopulations

Gnomad4 AFR exome

AF:

0.0213

Gnomad4 AMR exome

AF:

0.0471

Gnomad4 ASJ exome

AF:

0.0240

Gnomad4 EAS exome

AF:

0.0668

Gnomad4 SAS exome

AF:

0.0209

Gnomad4 FIN exome

AF:

0.0617

Gnomad4 NFE exome

AF:

0.0378

Gnomad4 OTH exome

AF:

0.0377

GnomAD4 genome

AF:

0.0807

AC:

6284

AN:

77828

Hom.:

191

Cov.:

AF XY:

0.0813

AC XY:

3062

AN XY:

37674

show subpopulations

Gnomad4 AFR

AF:

0.0472

Gnomad4 AMR

AF:

0.0845

Gnomad4 ASJ

AF:

0.0468

Gnomad4 EAS

AF:

0.102

Gnomad4 SAS

AF:

0.0328

Gnomad4 FIN

AF:

0.118

Gnomad4 NFE

AF:

0.0835

Gnomad4 OTH

AF:

0.0771

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 23, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over