15-74417377-G-C

Position:

• chr15-74417377-G-C

Variant summary

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

The NM_003612.5(SEMA7A):​c.619C>G​(p.Arg207Gly) 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. R207Q) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SEMA7A NM_003612.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304

Genes affected

SEMA7A (HGNC:10741): (semaphorin 7A (JohnMiltonHagen blood group)) This gene encodes a member of the semaphorin family of proteins. The encoded preproprotein is proteolytically processed to generate the mature glycosylphosphatidylinositol (GPI)-anchored membrane glycoprotein. The encoded protein is found on activated lymphocytes and erythrocytes and may be involved in immunomodulatory and neuronal processes. The encoded protein carries the John Milton Hagen (JMH) blood group antigens. Mutations in this gene may be associated with reduced bone mineral density (BMD). Alternative splicing results in multiple transcript variants, at least one of which encodes an isoform that is proteolytically processed. [provided by RefSeq, Feb 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=0.06442073).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SEMA7A	NM_003612.5	c.619C>G	p.Arg207Gly	missense_variant	6/14	ENST00000261918.9	NP_003603.1
SEMA7A	NM_001146029.3	c.577C>G	p.Arg193Gly	missense_variant	5/13		NP_001139501.1
SEMA7A	NM_001146030.3	c.124C>G	p.Arg42Gly	missense_variant	6/14		NP_001139502.1
SEMA7A	XM_047433177.1	c.496C>G	p.Arg166Gly	missense_variant	6/14		XP_047289133.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SEMA7A	ENST00000261918.9	c.619C>G	p.Arg207Gly	missense_variant	6/14	1	NM_003612.5	ENSP00000261918.4
SEMA7A	ENST00000543145.6	c.577C>G	p.Arg193Gly	missense_variant	5/13	2		ENSP00000438966.2
SEMA7A	ENST00000542748.6	c.124C>G	p.Arg42Gly	missense_variant	6/14	5		ENSP00000441493.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.19	T
BayesDel_noAF	Benign	-0.52
CADD	Benign	16
DANN	Benign	0.95
DEOGEN2	Benign	0.054	T;T;.
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.0
FATHMM_MKL	Benign	0.10	N
LIST_S2	Benign	0.72	T;T;T
M_CAP	Benign	0.014	T
MetaRNN	Benign	0.064	T;T;T
MetaSVM	Benign	-0.91	T
MutationAssessor	Benign	-0.61	N;.;.
PrimateAI	Benign	0.24	T
PROVEAN	Benign	1.3	N;N;N
REVEL	Benign	0.086
Sift	Benign	0.29	T;T;T
Sift4G	Benign	0.24	T;T;T
Polyphen		0.0010	B;.;.
Vest4		0.18
MutPred		0.50		Loss of methylation at R207 (P = 0.0404);.;.;
MVP		0.16
MPC		0.60
ClinPred		0.076	T
GERP RS		-0.60
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.46
gMVP		0.65

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: rs56367230; hg19: chr15-74709718;