chr7-84339187-C-T

Position:

• chr7-84339187-C-T

Variant summary

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

The ENST00000424555.5(SEMA3A):​c.-168-31895G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0145 in 151,780 control chromosomes in the GnomAD database, including 96 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 0.014 (96 hom., cov: 32)
• Consequence: SEMA3A ENST00000424555.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SEMA3A	XM_005250110.4	c.-168-31895G>A		intron_variant			XP_005250167.1
SEMA3A	XM_047419751.1	c.-258-31895G>A		intron_variant			XP_047275707.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SEMA3A	ENST00000448879.5	c.-168-31895G>A		intron_variant		5		ENSP00000402093.1
SEMA3A	ENST00000424555.5	c.-168-31895G>A		intron_variant		4		ENSP00000404800.1
SEMA3A	ENST00000471474.5	n.373-31895G>A		intron_variant		5
SEMA3A	ENST00000490883.1	n.152-31895G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0145 AC: 2201 AN: 151664 Hom.: 96 Cov.: 32

Gnomad AFR AF: 0.00228

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0515

Gnomad ASJ AF: 0.0207

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.0102

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00388

Gnomad OTH AF: 0.0187

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

GnomAD4 genome AF: 0.0145 AC: 2197 AN: 151780 Hom.: 96 Cov.: 32 AF XY: 0.0161 AC XY: 1196 AN XY: 74214

Gnomad4 AFR AF: 0.00228

Gnomad4 AMR AF: 0.0513

Gnomad4 ASJ AF: 0.0207

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.0104

Gnomad4 FIN AF: 0.0102

Gnomad4 NFE AF: 0.00388

Gnomad4 OTH AF: 0.0180

Alfa AF: 0.00327 Hom.: 1

Bravo AF: 0.0189

Asia WGS AF: 0.0690 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.2
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10488587; hg19: chr7-83968503;