2-39666147-G-T

Position:

• chr2-39666147-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_152390.3(TMEM178A):​c.173G>T​(p.Arg58Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: TMEM178A NM_152390.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.37

Genes affected

TMEM178A (HGNC:28517): (transmembrane protein 178A) Predicted to be involved in negative regulation of osteoclast differentiation and regulation of cytosolic calcium ion concentration. Predicted to be integral component of membrane. Predicted to be active in endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.27895737).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM178A	NM_152390.3	c.173G>T	p.Arg58Leu	missense_variant	1/4	ENST00000281961.3	NP_689603.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM178A	ENST00000281961.3	c.173G>T	p.Arg58Leu	missense_variant	1/4	1	NM_152390.3	ENSP00000281961	P1
TMEM178A	ENST00000437068.5	n.367+799G>T		intron_variant, non_coding_transcript_variant		4
TMEM178A	ENST00000482239.5	n.143+507G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 31

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 21, 2024

The c.173G>T (p.R58L) alteration is located in exon 1 (coding exon 1) of the TMEM178A gene. This alteration results from a G to T substitution at nucleotide position 173, causing the arginine (R) at amino acid position 58 to be replaced by a leucine (L). 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	Pathogenic	0.69
BayesDel_addAF	Benign	-0.044	T
BayesDel_noAF	Benign	-0.30
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.015	T;.
Eigen	Benign	0.17
Eigen_PC	Benign	0.098
FATHMM_MKL	Uncertain	0.78	D
LIST_S2	Benign	0.85	T;T
M_CAP	Pathogenic	0.76	D
MetaRNN	Benign	0.28	T;T
MetaSVM	Benign	-0.91	T
MutationAssessor	Benign	1.9	M;M
MutationTaster	Benign	1.0	D
PrimateAI	Pathogenic	0.97	D
PROVEAN	Benign	-1.2	N;.
REVEL	Benign	0.18
Sift	Benign	0.057	T;.
Sift4G	Benign	0.16	T;D
Polyphen		0.99	D;D
Vest4		0.30
MutPred		0.26		Loss of glycosylation at P53 (P = 0.1123);Loss of glycosylation at P53 (P = 0.1123);
MVP		0.043
MPC		1.1
ClinPred		0.85	D
GERP RS		2.5
Varity_R		0.11
gMVP		0.75

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-39893287;