rs16687

Variant names:

• chr7-84258560-TAC-T
• rs16687
• ENST00000864988.1:c.-83+36480_-83+36481delGT

Your query was ambiguous. Multiple possible variants found:

• chr7-84258560-TAC-T
• chr7-84258560-TAC-TACAC

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000424555.5(SEMA3A):​c.-83+48645_-83+48646delGT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.71 (38109 hom., cov: 0)
• Consequence: SEMA3A ENST00000424555.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 2 publications found

Genes affected

SEMA3A (HGNC:10723): (semaphorin 3A) This gene is a member of the semaphorin family and encodes a protein with an Ig-like C2-type (immunoglobulin-like) domain, a PSI domain and a Sema domain. This secreted protein can function as either a chemorepulsive agent, inhibiting axonal outgrowth, or as a chemoattractive agent, stimulating the growth of apical dendrites. In both cases, the protein is vital for normal neuronal pattern development. Increased expression of this protein is associated with schizophrenia and is seen in a variety of human tumor cell lines. Also, aberrant release of this protein is associated with the progression of Alzheimer's disease. [provided by RefSeq, Jul 2008]

SEMA3A Gene-Disease associations (from GenCC):

• skeletal dysplasia

  Inheritance: AR Classification: DEFINITIVE Submitted by: G2P
• hypogonadotropic hypogonadism 16 with or without anosmia

  Inheritance: AD, SD Classification: STRONG, LIMITED Submitted by: Ambry Genetics, PanelApp Australia, Labcorp Genetics (formerly Invitae)
• multiple congenital anomalies/dysmorphic syndrome

  Inheritance: AR Classification: MODERATE Submitted by: Ambry Genetics
• Brugada syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Kallmann syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000424555.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SEMA3A	ENST00000864988.1		c.-83+36480_-83+36481delGT		intron	N/A	ENSP00000535047.1
	SEMA3A	ENST00000864989.1		c.-83+36480_-83+36481delGT		intron	N/A	ENSP00000535048.1
	SEMA3A	ENST00000864990.1		c.-83+36480_-83+36481delGT		intron	N/A	ENSP00000535049.1

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107201 AN: 151720 Hom.: 38083 Cov.: 0

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.696

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.707 AC: 107275 AN: 151838 Hom.: 38109 Cov.: 0 AF XY: 0.704 AC XY: 52222 AN XY: 74170

African (AFR) AF: 0.756 AC: 31298 AN: 41408

American (AMR) AF: 0.621 AC: 9475 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2298 AN: 3468

East Asian (EAS) AF: 0.788 AC: 4067 AN: 5160

South Asian (SAS) AF: 0.670 AC: 3224 AN: 4814

European-Finnish (FIN) AF: 0.653 AC: 6853 AN: 10494

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47758 AN: 67944

Other (OTH) AF: 0.700 AC: 1472 AN: 2102

Alfa AF: 0.706 Hom.: 4673

Bravo AF: 0.705

Asia WGS AF: 0.747 AC: 2596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs16687; hg19: chr7-83887876;