rs17158675

chr7-84153523-G-A

Variant summary

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

The NM_006080.3(SEMA3A):c.113-18572C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0771 in 152,066 control chromosomes in the GnomAD database, including 773 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 0.077 (773 hom., cov: 32)
• Consequence: SEMA3A NM_006080.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SEMA3A	NM_006080.3	c.113-18572C>T		intron_variant		ENST00000265362.9
SEMA3A	XM_005250110.4	c.113-18572C>T		intron_variant
SEMA3A	XM_047419751.1	c.113-18572C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SEMA3A	ENST00000265362.9	c.113-18572C>T		intron_variant		1	NM_006080.3	P1
SEMA3A	ENST00000420047.1	c.113-18572C>T		intron_variant		4
SEMA3A	ENST00000436949.5	c.113-18572C>T		intron_variant		5		P1

Frequencies

GnomAD3 genomes AF: 0.0770 AC: 11700 AN: 151948 Hom.: 770 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.0449

Gnomad ASJ AF: 0.0774

Gnomad EAS AF: 0.0220

Gnomad SAS AF: 0.0759

Gnomad FIN AF: 0.0236

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0407

Gnomad OTH AF: 0.0733

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

GnomAD4 genome AF: 0.0771 AC: 11718 AN: 152066 Hom.: 773 Cov.: 32 AF XY: 0.0756 AC XY: 5620 AN XY: 74366

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.0448

Gnomad4 ASJ AF: 0.0774

Gnomad4 EAS AF: 0.0220

Gnomad4 SAS AF: 0.0755

Gnomad4 FIN AF: 0.0236

Gnomad4 NFE AF: 0.0407

Gnomad4 OTH AF: 0.0769

Alfa AF: 0.0476 Hom.: 316

Bravo AF: 0.0837

Asia WGS AF: 0.0610 AC: 212 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	5.4
Dann	Benign	0.28

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: rs17158675; hg19: chr7-83782839;