Variant chr13-113804913-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_182614.4(TMEM255B):c.698C>T(p.Pro233Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00506 in 1,602,896 control chromosomes in the GnomAD database, including 41 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0034 ( 3 hom., cov: 33)

Exomes 𝑓: 0.0052 ( 38 hom. )

Consequence

TMEM255B
NM_182614.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.27

Variant links:

Genes affected

TMEM255B (HGNC:28297): (transmembrane protein 255B) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM255B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004901707).

BP6

Variant 13-113804913-C-T is Benign according to our data. Variant chr13-113804913-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3025042.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM255B	NM_182614.4 linkuse as main transcript	c.698C>T	p.Pro233Leu	missense_variant	8/9	ENST00000375353.5
TMEM255B	NM_001348663.2 linkuse as main transcript	c.669+3101C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
TMEM255B	ENST00000375353.5 linkuse as main transcript	c.698C>T	p.Pro233Leu	missense_variant	8/9	1	NM_182614.4	P1
TMEM255B	ENST00000467169.1 linkuse as main transcript	n.312C>T		non_coding_transcript_exon_variant	2/3	3
TMEM255B	ENST00000498692.1 linkuse as main transcript			downstream_gene_variant		5

Frequencies

GnomAD3 genomes

AF:

0.00344

AC:

524

AN:

152150

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00123

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00412

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.000753

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00565

Gnomad OTH

AF:

0.00670

GnomAD3 exomes

AF:

0.00363

AC:

876

AN:

241506

Hom.:

AF XY:

0.00380

AC XY:

499

AN XY:

131392

show subpopulations

Gnomad AFR exome

AF:

0.00106

Gnomad AMR exome

AF:

0.00263

Gnomad ASJ exome

AF:

0.000402

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000826

Gnomad FIN exome

AF:

0.00191

Gnomad NFE exome

AF:

0.00614

Gnomad OTH exome

AF:

0.00403

GnomAD4 exome

AF:

0.00523

AC:

7585

AN:

1450628

Hom.:

Cov.:

AF XY:

0.00512

AC XY:

3693

AN XY:

721982

show subpopulations

Gnomad4 AFR exome

AF:

0.000957

Gnomad4 AMR exome

AF:

0.00296

Gnomad4 ASJ exome

AF:

0.000307

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000768

Gnomad4 FIN exome

AF:

0.00176

Gnomad4 NFE exome

AF:

0.00634

Gnomad4 OTH exome

AF:

0.00320

GnomAD4 genome

AF:

0.00344

AC:

524

AN:

152268

Hom.:

Cov.:

AF XY:

0.00325

AC XY:

242

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.00123

Gnomad4 AMR

AF:

0.00412

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000621

Gnomad4 FIN

AF:

0.000753

Gnomad4 NFE

AF:

0.00565

Gnomad4 OTH

AF:

0.00663

Alfa

AF:

0.00496

Hom.:

Bravo

AF:

0.00350

ESP6500AA

AF:

0.00136

AC:

ESP6500EA

AF:

0.00593

AC:

ExAC

AF:

0.00350

AC:

424

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00706

EpiControl

AF:

0.00744

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2024

TMEM255B: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.075

BayesDel_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.51

CADD

Benign

9.8

DANN

Uncertain

0.98

DEOGEN2

Benign

0.045

Eigen

Benign

-0.35

Eigen_PC

Benign

-0.47

FATHMM_MKL

Benign

0.65

LIST_S2

Benign

0.77

M_CAP

Benign

0.011

MetaRNN

Benign

0.0049

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.8

MutationTaster

Benign

0.99

PrimateAI

Benign

0.36

PROVEAN

Uncertain

-4.2

REVEL

Benign

0.084

Sift

Uncertain

0.024

Sift4G

Uncertain

0.040

Polyphen

0.67

Vest4

0.29

MVP

0.25

MPC

0.072

ClinPred

0.021

GERP RS

1.6

Varity_R

0.11

gMVP

0.33

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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