Genetic Variant TMBIM4:p.Ser25Phe (chr12-66169878-G-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_016056.4(TMBIM4):c.74C>T(p.Ser25Phe) variant causes a missense change. The variant allele was found at a frequency of 0.000467 in 1,505,420 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00031 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00048 ( 4 hom. )

Consequence

TMBIM4
NM_016056.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.23

Variant links:

Genes affected

TMBIM4 (HGNC:24257): (transmembrane BAX inhibitor motif containing 4) Involved in negative regulation of apoptotic process and regulation of calcium-mediated signaling. Located in Golgi stack. [provided by Alliance of Genome Resources, Apr 2022]

TMBIM4 links:

ENSG00000228144 (HGNC:):

ENSG00000228144 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.033810467).

BS2

High Homozygotes in GnomAdExome4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMBIM4	NM_016056.4 link	c.74C>T	p.Ser25Phe	missense_variant	Exon 1 of 7	ENST00000358230.8	NP_057140.2	Q9HC24
TMBIM4	NM_001282606.2 link	c.74C>T	p.Ser25Phe	missense_variant	Exon 1 of 8		NP_001269535.1	Q9HC24G3XAA5Q9HC19
TMBIM4	NM_001282610.2 link	c.19C>T	p.Pro7Ser	missense_variant	Exon 1 of 7		NP_001269539.1	Q9HC24Q7Z782
TMBIM4	NM_001282609.2 link	c.74C>T	p.Ser25Phe	missense_variant	Exon 1 of 7		NP_001269538.1	Q9HC24G3V1M2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMBIM4	ENST00000358230.8 link	c.74C>T	p.Ser25Phe	missense_variant	Exon 1 of 7	1	NM_016056.4	ENSP00000350965.3		Q9HC24
ENSG00000228144	ENST00000539652.1 link	n.74C>T		non_coding_transcript_exon_variant	Exon 1 of 8	2		ENSP00000454670.1		F6UZH7

Frequencies

GnomAD3 genomes

AF:

0.000309

AC:

AN:

152236

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000262

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.000188

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000470

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.000601

AC:

AN:

106526

Hom.:

AF XY:

0.000738

AC XY:

AN XY:

58274

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000413

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00203

Gnomad FIN exome

AF:

0.000276

Gnomad NFE exome

AF:

0.000315

Gnomad OTH exome

AF:

0.00106

GnomAD4 exome

AF:

0.000485

AC:

656

AN:

1353066

Hom.:

Cov.:

AF XY:

0.000558

AC XY:

372

AN XY:

667172

show subpopulations

Gnomad4 AFR exome

AF:

0.0000733

Gnomad4 AMR exome

AF:

0.000346

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00189

Gnomad4 FIN exome

AF:

0.000493

Gnomad4 NFE exome

AF:

0.000404

Gnomad4 OTH exome

AF:

0.000465

GnomAD4 genome

AF:

0.000308

AC:

AN:

152354

Hom.:

Cov.:

AF XY:

0.000336

AC XY:

AN XY:

74494

show subpopulations

Gnomad4 AFR

AF:

0.0000240

Gnomad4 AMR

AF:

0.000261

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.000188

Gnomad4 NFE

AF:

0.000470

Gnomad4 OTH

AF:

0.000473

Alfa

AF:

0.000737

Hom.:

Bravo

AF:

0.000272

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000386

AC:

ExAC

AF:

0.000280

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Jun 06, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.74C>T (p.S25F) alteration is located in exon 1 (coding exon 1) of the TMBIM4 gene. This alteration results from a C to T substitution at nucleotide position 74, causing the serine (S) at amino acid position 25 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.40

BayesDel_addAF

Benign

-0.46

BayesDel_noAF

Uncertain

-0.060

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Benign

0.14

T;.;.;.;.;.;.

Eigen

Uncertain

0.50

Eigen_PC

Uncertain

0.49

FATHMM_MKL

Benign

0.54

LIST_S2

Uncertain

0.93

D;D;D;D;D;D;D

M_CAP

Pathogenic

0.31

MetaRNN

Benign

0.034

T;T;T;T;T;T;T

MetaSVM

Benign

-0.89

MutationAssessor

Uncertain

2.2

M;.;.;.;.;.;.

PrimateAI

Uncertain

0.67

PROVEAN

Uncertain

-3.6

D;.;D;D;.;D;.

REVEL

Benign

0.19

Sift

Uncertain

0.0040

D;.;D;D;.;D;.

Sift4G

Uncertain

0.023

D;T;T;D;T;T;D

Polyphen

0.99

D;.;D;D;.;.;.

Vest4

0.54

MVP

0.56

MPC

0.82

ClinPred

0.098

GERP RS

4.6

Varity_R

0.57

gMVP

0.28

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