rs16687

Variant names:

• chr7-84258560-TAC-T
• rs16687
• ENST00000448879.5:c.-83+48645_-83+48646delGT

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SEMA3A	XM_005250110.4	c.-83+48645_-83+48646delGT		intron_variant	Intron 3 of 19		XP_005250167.1
SEMA3A	XM_047419751.1	c.-83+36480_-83+36481delGT		intron_variant	Intron 4 of 20		XP_047275707.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SEMA3A	ENST00000448879.5	c.-83+48645_-83+48646delGT		intron_variant	Intron 4 of 4	5		ENSP00000402093.1
SEMA3A	ENST00000424555.5	c.-83+48645_-83+48646delGT		intron_variant	Intron 3 of 3	4		ENSP00000404800.1

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

Gnomad4 AFR AF: 0.756

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.788

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.700

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 v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16687; hg19: chr7-83887876;