rs10235789

chr7-84027484-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006080.3(SEMA3A):c.668-13133A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 152,036 control chromosomes in the GnomAD database, including 12,868 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.39 (12868 hom., cov: 32)
• Consequence: SEMA3A NM_006080.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SEMA3A	NM_006080.3	c.668-13133A>G		intron_variant		ENST00000265362.9
SEMA3A	XM_005250110.4	c.668-13133A>G		intron_variant
SEMA3A	XM_047419751.1	c.668-13133A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SEMA3A	ENST00000265362.9	c.668-13133A>G		intron_variant		1	NM_006080.3	P1
SEMA3A	ENST00000436949.5	c.668-13133A>G		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59241 AN: 151918 Hom.: 12863 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.390 AC: 59269 AN: 152036 Hom.: 12868 Cov.: 32 AF XY: 0.387 AC XY: 28741 AN XY: 74304

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.418

Alfa AF: 0.475 Hom.: 32073

Bravo AF: 0.378

Asia WGS AF: 0.228 AC: 792 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	3.3
Dann	Benign	0.77

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: rs10235789; hg19: chr7-83656800;