NM_198153.3:c.311C>G

Variant names:

• chr6-41228961-C-G
• NM_198153.3:c.311C>G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_198153.3(TREML4):​c.311C>G​(p.Ser104Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S104L) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: TREML4 NM_198153.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

Genes affected

TREML4 (HGNC:30807): (triggering receptor expressed on myeloid cells like 4) Predicted to enable signaling receptor activity. Involved in positive regulation of toll-like receptor 7 signaling pathway. Predicted to be located in endoplasmic reticulum. Predicted to be active in cell surface. Predicted to colocalize with endosome membrane and lysosomal membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TREML4	NM_198153.3	c.311C>G	p.Ser104Trp	missense_variant	Exon 2 of 6	ENST00000341495.7	NP_937796.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TREML4	ENST00000341495.7	c.311C>G	p.Ser104Trp	missense_variant	Exon 2 of 6	1	NM_198153.3	ENSP00000342570.2
TREML4	ENST00000448827.6	c.311C>G	p.Ser104Trp	missense_variant	Exon 2 of 6	1		ENSP00000418078.1
TREML4	ENST00000461240.1	n.5C>G		non_coding_transcript_exon_variant	Exon 1 of 6	2		ENSP00000418480.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 55

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.64
BayesDel_addAF	Benign	0.011	T
BayesDel_noAF	Benign	-0.22
CADD	Benign	18
DANN	Uncertain	0.98
DEOGEN2	Benign	0.38	T;T
Eigen	Benign	-0.22
Eigen_PC	Benign	-0.53
FATHMM_MKL	Benign	0.098	N
LIST_S2	Benign	0.73	.;T
M_CAP	Benign	0.027	D
MetaRNN	Uncertain	0.63	D;D
MetaSVM	Benign	-0.71	T
MutationAssessor	Uncertain	2.5	M;M
PrimateAI	Benign	0.28	T
PROVEAN	Pathogenic	-6.4	D;D
REVEL	Uncertain	0.29
Sift	Pathogenic	0.0	D;D
Sift4G	Pathogenic	0.0010	D;D
Polyphen		1.0	D;D
Vest4		0.43
MutPred		0.65		Loss of glycosylation at S104 (P = 0.0142);Loss of glycosylation at S104 (P = 0.0142);
MVP		0.35
MPC		0.23
ClinPred		0.74	D
GERP RS		-0.36
Varity_R		0.67
gMVP		0.54

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: chr6-41196699; COSMIC: COSV58384757;