3-50185493-T-G

Variant names:

• chr3-50185493-T-G
• rs1046956
• NM_004186.5:c.1507T>G

Variant summary

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

The NM_004186.5(SEMA3F):​c.1507T>G​(p.Leu503Val) 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. 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. L503M) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 30)
• Consequence: SEMA3F NM_004186.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

Genes affected

SEMA3F (HGNC:10728): (semaphorin 3F) This gene encodes a member of the semaphorin III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin loop and a C-terminal basic domain. This gene is expressed by the endothelial cells where it was found to act in an autocrine fashion to induce apoptosis, inhibit cell proliferation and survival, and function as an anti-tumorigenic agent. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]

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=0.032608747).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEMA3F	NM_004186.5	c.1507T>G	p.Leu503Val	missense_variant	Exon 14 of 19	ENST00000002829.8	NP_004177.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEMA3F	ENST00000002829.8	c.1507T>G	p.Leu503Val	missense_variant	Exon 14 of 19	1	NM_004186.5	ENSP00000002829.3
SEMA3F	ENST00000434342.5	c.1414T>G	p.Leu472Val	missense_variant	Exon 13 of 18	1		ENSP00000409859.1
SEMA3F	ENST00000413852.5	c.1210T>G	p.Leu404Val	missense_variant	Exon 13 of 18	1		ENSP00000388931.1
SEMA3F	ENST00000470737.1	n.*28T>G		downstream_gene_variant		5

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 56

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.077
BayesDel_addAF	Benign	-0.35	T
BayesDel_noAF	Benign	-0.75
CADD	Benign	16
DANN	Benign	0.69
DEOGEN2	Benign	0.0098	T;T;.
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.38	N
LIST_S2	Benign	0.35	T;T;T
M_CAP	Benign	0.0035	T
MetaRNN	Benign	0.033	T;T;T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	0.20	.;N;.
PrimateAI	Benign	0.30	T
PROVEAN	Benign	-0.40	N;N;N
REVEL	Benign	0.045
Sift	Benign	0.41	T;T;T
Sift4G	Benign	0.46	T;T;T
Polyphen		0.0	.;B;.
Vest4		0.047
MutPred		0.36		.;Gain of catalytic residue at L503 (P = 0.0022);.;
MVP		0.14
MPC		0.81
ClinPred		0.037	T
GERP RS		0.29
Varity_R		0.022
gMVP		0.069

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

Other links and lift over

dbSNP: rs1046956; hg19: chr3-50222926;