Variant rs6116651 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001009923.2(TMEM230):c.306T>A(p.Pro102=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 1,606,410 control chromosomes in the GnomAD database, including 12,030 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 2445 hom., cov: 32)

Exomes 𝑓: 0.11 ( 9585 hom. )

Consequence

TMEM230
NM_001009923.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.668

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BP6

Variant 20-5106293-A-T is Benign according to our data. Variant chr20-5106293-A-T is described in ClinVar as [Benign]. Clinvar id is 1265859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.668 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.291 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.306T>A	p.Pro102=	synonymous_variant	4/5	ENST00000342308.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM230	ENST00000342308.10 linkuse as main transcript	c.306T>A	p.Pro102=	synonymous_variant	4/5	2	NM_001009923.2		Q96A57-2

Frequencies

GnomAD3 genomes

AF:

0.152

AC:

23120

AN:

152060

Hom.:

2441

Cov.:

show subpopulations

Gnomad AFR

AF:

0.296

Gnomad AMI

AF:

0.132

Gnomad AMR

AF:

0.108

Gnomad ASJ

AF:

0.147

Gnomad EAS

AF:

0.000769

Gnomad SAS

AF:

0.0555

Gnomad FIN

AF:

0.0595

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.108

Gnomad OTH

AF:

0.150

GnomAD3 exomes

AF:

0.0997

AC:

24264

AN:

243446

Hom.:

1717

AF XY:

0.0964

AC XY:

12697

AN XY:

131664

show subpopulations

Gnomad AFR exome

AF:

0.299

Gnomad AMR exome

AF:

0.0665

Gnomad ASJ exome

AF:

0.146

Gnomad EAS exome

AF:

0.000112

Gnomad SAS exome

AF:

0.0581

Gnomad FIN exome

AF:

0.0655

Gnomad NFE exome

AF:

0.110

Gnomad OTH exome

AF:

0.102

GnomAD4 exome

AF:

0.107

AC:

155483

AN:

1454232

Hom.:

9585

Cov.:

AF XY:

0.105

AC XY:

76158

AN XY:

723318

show subpopulations

Gnomad4 AFR exome

AF:

0.308

Gnomad4 AMR exome

AF:

0.0717

Gnomad4 ASJ exome

AF:

0.152

Gnomad4 EAS exome

AF:

0.000126

Gnomad4 SAS exome

AF:

0.0621

Gnomad4 FIN exome

AF:

0.0685

Gnomad4 NFE exome

AF:

0.110

Gnomad4 OTH exome

AF:

0.115

GnomAD4 genome

AF:

0.152

AC:

23150

AN:

152178

Hom.:

2445

Cov.:

AF XY:

0.149

AC XY:

11062

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.296

Gnomad4 AMR

AF:

0.108

Gnomad4 ASJ

AF:

0.147

Gnomad4 EAS

AF:

0.000771

Gnomad4 SAS

AF:

0.0558

Gnomad4 FIN

AF:

0.0595

Gnomad4 NFE

AF:

0.108

Gnomad4 OTH

AF:

0.149

Alfa

AF:

0.124

Hom.:

477

Bravo

AF:

0.162

Asia WGS

AF:

0.0450

AC:

158

AN:

3478

EpiCase

AF:

0.114

EpiControl

AF:

0.118

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 05, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

7.0

DANN

Benign

0.73

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

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