Variant rs7809708 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006080.3(SEMA3A):c.1860+30A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 1,606,842 control chromosomes in the GnomAD database, including 54,156 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5528 hom., cov: 32)

Exomes 𝑓: 0.25 ( 48628 hom. )

Consequence

SEMA3A
NM_006080.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.162

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 7-83963175-T-C is Benign according to our data. Variant chr7-83963175-T-C is described in ClinVar as [Benign]. Clinvar id is 1292758.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
SEMA3A	NM_006080.3 link	c.1860+30A>G	intron_variant	ENST00000265362.9	NP_006071.1	Q14563
SEMA3A	XM_005250110.4 link	c.1860+30A>G	intron_variant		XP_005250167.1	Q14563
SEMA3A	XM_047419751.1 link	c.1860+30A>G	intron_variant		XP_047275707.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SEMA3A	ENST00000265362.9 link	c.1860+30A>G		intron_variant		1	NM_006080.3	ENSP00000265362.3		Q14563
SEMA3A	ENST00000436949.5 link	c.1860+30A>G		intron_variant		5		ENSP00000415260.1		Q14563

Frequencies

GnomAD3 genomes

AF:

0.264

AC:

40120

AN:

152000

Hom.:

5527

Cov.:

show subpopulations

Gnomad AFR

AF:

0.311

Gnomad AMI

AF:

0.305

Gnomad AMR

AF:

0.213

Gnomad ASJ

AF:

0.235

Gnomad EAS

AF:

0.0424

Gnomad SAS

AF:

0.169

Gnomad FIN

AF:

0.271

Gnomad MID

AF:

0.358

Gnomad NFE

AF:

0.269

Gnomad OTH

AF:

0.289

GnomAD3 exomes

AF:

0.225

AC:

56125

AN:

249096

Hom.:

7105

AF XY:

0.227

AC XY:

30629

AN XY:

134870

show subpopulations

Gnomad AFR exome

AF:

0.316

Gnomad AMR exome

AF:

0.148

Gnomad ASJ exome

AF:

0.228

Gnomad EAS exome

AF:

0.0452

Gnomad SAS exome

AF:

0.172

Gnomad FIN exome

AF:

0.264

Gnomad NFE exome

AF:

0.271

Gnomad OTH exome

AF:

0.247

GnomAD4 exome

AF:

0.253

AC:

367587

AN:

1454724

Hom.:

48628

Cov.:

AF XY:

0.252

AC XY:

182512

AN XY:

724116

show subpopulations

Gnomad4 AFR exome

AF:

0.320

Gnomad4 AMR exome

AF:

0.159

Gnomad4 ASJ exome

AF:

0.225

Gnomad4 EAS exome

AF:

0.0312

Gnomad4 SAS exome

AF:

0.176

Gnomad4 FIN exome

AF:

0.262

Gnomad4 NFE exome

AF:

0.268

Gnomad4 OTH exome

AF:

0.249

GnomAD4 genome

AF:

0.264

AC:

40142

AN:

152118

Hom.:

5528

Cov.:

AF XY:

0.261

AC XY:

19401

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.311

Gnomad4 AMR

AF:

0.213

Gnomad4 ASJ

AF:

0.235

Gnomad4 EAS

AF:

0.0427

Gnomad4 SAS

AF:

0.170

Gnomad4 FIN

AF:

0.271

Gnomad4 NFE

AF:

0.269

Gnomad4 OTH

AF:

0.288

Alfa

AF:

0.263

Hom.:

1045

Bravo

AF:

0.263

Asia WGS

AF:

0.137

AC:

479

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 09, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

5.4

DANN

Benign

0.65

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over