14-24316687-C-G

Variant names:

• chr14-24316687-C-G
• NM_001143919.3:c.1036C>G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001143919.3(LTB4R):​c.1036C>G​(p.Leu346Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000144 in 1,385,828 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. 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. L346F) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: LTB4R NM_001143919.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39

Genes affected

LTB4R (HGNC:6713): (leukotriene B4 receptor) Predicted to enable G protein-coupled peptide receptor activity and leukotriene B4 receptor activity. Predicted to be involved in inflammatory response and neuropeptide signaling pathway. Predicted to act upstream of or within signal transduction. Predicted to be located in plasma membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.0630905).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LTB4R	NM_001143919.3	c.1036C>G	p.Leu346Val	missense_variant	Exon 2 of 2	ENST00000345363.8	NP_001137391.1
LTB4R	NM_181657.3	c.1036C>G	p.Leu346Val	missense_variant	Exon 2 of 2		NP_858043.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LTB4R	ENST00000345363.8	c.1036C>G	p.Leu346Val	missense_variant	Exon 2 of 2	1	NM_001143919.3	ENSP00000307445.3
LTB4R	ENST00000396782.2	c.1036C>G	p.Leu346Val	missense_variant	Exon 2 of 2	1		ENSP00000380002.2
LTB4R	ENST00000396789.4	c.1036C>G	p.Leu346Val	missense_variant	Exon 2 of 2	1		ENSP00000380008.4
LTB4R	ENST00000556141.1	c.*40C>G		downstream_gene_variant		3		ENSP00000451929.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000144 AC: 2 AN: 1385828 Hom.: 0 Cov.: 32 AF XY: 0.00000292 AC XY: 2 AN XY: 684742

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000186

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.065
BayesDel_addAF	Benign	-0.19	T
BayesDel_noAF	Benign	-0.51
CADD	Benign	16
DANN	Uncertain	0.99
DEOGEN2	Benign	0.069	T;T;T
Eigen	Benign	-0.74
Eigen_PC	Benign	-0.78
FATHMM_MKL	Benign	0.20	N
M_CAP	Benign	0.037	D
MetaRNN	Benign	0.063	T;T;T
MetaSVM	Benign	-0.90	T
MutationAssessor	Benign	0.90	L;L;L
PrimateAI	Benign	0.35	T
PROVEAN	Benign	0.23	N;N;N
REVEL	Benign	0.10
Sift	Benign	0.36	T;T;T
Sift4G	Uncertain	0.038	D;D;D
Polyphen		0.075	B;B;B
Vest4		0.11
MutPred		0.088		Gain of methylation at K347 (P = 0.0367);Gain of methylation at K347 (P = 0.0367);Gain of methylation at K347 (P = 0.0367);
MVP		0.43
MPC		1.7
ClinPred		0.096	T
GERP RS		2.4
Varity_R		0.033
gMVP		0.19

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: chr14-24785893;