Variant chr20-5106074-GACAAACAC-G 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+106_411+113del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 1,158,486 control chromosomes in the GnomAD database, including 5,444 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.10 ( 885 hom., cov: 0)

Exomes 𝑓: 0.12 ( 4559 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 20-5106074-GACAAACAC-G is Benign according to our data. Variant chr20-5106074-GACAAACAC-G is described in ClinVar as [Benign]. Clinvar id is 1245471.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 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+106_411+113del		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+106_411+113del		intron_variant		2	NM_001009923.2		Q96A57-2

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

13041

AN:

126342

Hom.:

885

Cov.:

show subpopulations

Gnomad AFR

AF:

0.180

Gnomad AMI

AF:

0.0192

Gnomad AMR

AF:

0.0656

Gnomad ASJ

AF:

0.0670

Gnomad EAS

AF:

0.0274

Gnomad SAS

AF:

0.0820

Gnomad FIN

AF:

0.103

Gnomad MID

AF:

0.0664

Gnomad NFE

AF:

0.0705

Gnomad OTH

AF:

0.0921

GnomAD4 exome

AF:

0.115

AC:

118981

AN:

1032050

Hom.:

4559

AF XY:

0.118

AC XY:

60508

AN XY:

511124

show subpopulations

Gnomad4 AFR exome

AF:

0.165

Gnomad4 AMR exome

AF:

0.0730

Gnomad4 ASJ exome

AF:

0.147

Gnomad4 EAS exome

AF:

0.106

Gnomad4 SAS exome

AF:

0.177

Gnomad4 FIN exome

AF:

0.106

Gnomad4 NFE exome

AF:

0.111

Gnomad4 OTH exome

AF:

0.118

GnomAD4 genome

AF:

0.103

AC:

13048

AN:

126436

Hom.:

885

Cov.:

AF XY:

0.105

AC XY:

6388

AN XY:

60694

show subpopulations

Gnomad4 AFR

AF:

0.179

Gnomad4 AMR

AF:

0.0654

Gnomad4 ASJ

AF:

0.0670

Gnomad4 EAS

AF:

0.0272

Gnomad4 SAS

AF:

0.0812

Gnomad4 FIN

AF:

0.103

Gnomad4 NFE

AF:

0.0704

Gnomad4 OTH

AF:

0.0916

Alfa

AF:

0.0817

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 19, 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