Variant 20-5106074-GACAAACACAC-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001009923.2(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
NM_001009923.2 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 20-5106074-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	Protein	UniProt
TMEM230	NM_001009923.2 linkuse as main transcript	c.411+104_411+113del		intron_variant		ENST00000342308.10	NP_001009923.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM230	ENST00000342308.10 linkuse as main transcript	c.411+104_411+113del		intron_variant		2	NM_001009923.2	ENSP00000341364		Q96A57-2

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

12740

AN:

126394

Hom.:

1572

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.0996

AC XY:

6047

AN XY:

60728

show subpopulations

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.:

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 21, 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