Variant 16-75539986-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001077418.3(TMEM231):c.*8A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 1,599,648 control chromosomes in the GnomAD database, including 52,187 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 4830 hom., cov: 32)

Exomes 𝑓: 0.25 ( 47357 hom. )

Consequence

TMEM231
NM_001077418.3 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.467

Variant links:

Genes affected

TMEM231 (HGNC:37234): (transmembrane protein 231) This gene encodes a transmembrane protein, which is a component of the B9 complex involved in the formation of the diffusion barrier between the cilia and plasma membrane. Mutations in this gene cause Joubert syndrome (JBTS). Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2013]

TMEM231 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BP6

Variant 16-75539986-T-C is Benign according to our data. Variant chr16-75539986-T-C is described in ClinVar as [Benign]. Clinvar id is 257328.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-75539986-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
TMEM231	NM_001077418.3 linkuse as main transcript	c.*8A>G	3_prime_UTR_variant	7/7	ENST00000258173.11
TMEM231	NM_001077416.2 linkuse as main transcript	c.*8A>G	3_prime_UTR_variant	6/6
TMEM231	NR_074083.2 linkuse as main transcript	n.1125A>G	non_coding_transcript_exon_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM231	ENST00000258173.11 linkuse as main transcript	c.*8A>G		3_prime_UTR_variant	7/7	1	NM_001077418.3	P1	Q9H6L2-1

Frequencies

GnomAD3 genomes

AF:

0.252

AC:

37791

AN:

149860

Hom.:

4826

Cov.:

show subpopulations

Gnomad AFR

AF:

0.255

Gnomad AMI

AF:

0.348

Gnomad AMR

AF:

0.182

Gnomad ASJ

AF:

0.174

Gnomad EAS

AF:

0.228

Gnomad SAS

AF:

0.225

Gnomad FIN

AF:

0.308

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.264

Gnomad OTH

AF:

0.230

GnomAD3 exomes

AF:

0.234

AC:

56179

AN:

240376

Hom.:

7030

AF XY:

0.237

AC XY:

30826

AN XY:

130168

show subpopulations

Gnomad AFR exome

AF:

0.246

Gnomad AMR exome

AF:

0.119

Gnomad ASJ exome

AF:

0.168

Gnomad EAS exome

AF:

0.201

Gnomad SAS exome

AF:

0.229

Gnomad FIN exome

AF:

0.303

Gnomad NFE exome

AF:

0.266

Gnomad OTH exome

AF:

0.241

GnomAD4 exome

AF:

0.252

AC:

365984

AN:

1449680

Hom.:

47357

Cov.:

AF XY:

0.252

AC XY:

181851

AN XY:

720562

show subpopulations

Gnomad4 AFR exome

AF:

0.246

Gnomad4 AMR exome

AF:

0.127

Gnomad4 ASJ exome

AF:

0.176

Gnomad4 EAS exome

AF:

0.215

Gnomad4 SAS exome

AF:

0.229

Gnomad4 FIN exome

AF:

0.309

Gnomad4 NFE exome

AF:

0.260

Gnomad4 OTH exome

AF:

0.246

GnomAD4 genome

AF:

0.252

AC:

37817

AN:

149968

Hom.:

4830

Cov.:

AF XY:

0.251

AC XY:

18380

AN XY:

73354

show subpopulations

Gnomad4 AFR

AF:

0.255

Gnomad4 AMR

AF:

0.182

Gnomad4 ASJ

AF:

0.174

Gnomad4 EAS

AF:

0.227

Gnomad4 SAS

AF:

0.224

Gnomad4 FIN

AF:

0.308

Gnomad4 NFE

AF:

0.264

Gnomad4 OTH

AF:

0.233

Alfa

AF:

0.249

Hom.:

2145

Asia WGS

AF:

0.284

AC:

983

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 22, 2016	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.068

DANN

Benign

0.33

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