3-50269320-GC-GCCCCCCCCCCCC

Variant names:

• chr3-50269320-G-GCCCCCCCCCCC
• rs67324803
• NM_001290060.2:c.86_87insCCCCCCCCCCC

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001290061.1(SEMA3B):​c.86_87insCCCCCCCCCCC​(p.Arg30ProfsTer89) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SEMA3B NM_001290061.1 frameshift
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 0 publications found

Genes affected

SEMA3B (HGNC:10724): (semaphorin 3B) The protein encoded by this gene belongs to the class-3 semaphorin/collapsin family, whose members function in growth cone guidance during neuronal development. This family member inhibits axonal extension and has been shown to act as a tumor suppressor by inducing apoptosis. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Feb 2014]

SEMA3B-AS1 (HGNC:49096): (SEMA3B antisense RNA 1 (head to head))

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001290061.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SEMA3B	NM_001290060.2	MANE Select	c.86_87insCCCCCCCCCCC	p.Arg30ProfsTer89	frameshift	Exon 1 of 17	NP_001276989.1
	SEMA3B	NM_001290061.1		c.86_87insCCCCCCCCCCC	p.Arg30ProfsTer89	frameshift	Exon 1 of 17	NP_001276990.1
	SEMA3B	NM_001435956.1		c.86_87insCCCCCCCCCCC	p.Arg30ProfsTer89	frameshift	Exon 4 of 20	NP_001422885.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SEMA3B	ENST00000616701.5	TSL:1 MANE Select	c.86_87insCCCCCCCCCCC	p.Arg30ProfsTer89	frameshift	Exon 1 of 17	ENSP00000484146.1
	SEMA3B	ENST00000611067.4	TSL:1	c.86_87insCCCCCCCCCCC	p.Arg30ProfsTer89	frameshift	Exon 1 of 17	ENSP00000480680.1
	SEMA3B	ENST00000433753.4	TSL:1	c.86_87insCCCCCCCCCCC	p.Arg30ProfsTer89	frameshift	Exon 1 of 17	ENSP00000485281.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.055

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs67324803; hg19: chr3-50306752;