Variant 7-84005397-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_006080.3(SEMA3A):c.1302T>C(p.Ile434=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 1,612,230 control chromosomes in the GnomAD database, including 44,417 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.24 ( 4649 hom., cov: 31)

Exomes 𝑓: 0.23 ( 39768 hom. )

Consequence

SEMA3A
NM_006080.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.274

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP6

Variant 7-84005397-A-G is Benign according to our data. Variant chr7-84005397-A-G is described in ClinVar as [Benign]. Clinvar id is 1289263.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-84005397-A-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.274 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
SEMA3A	NM_006080.3 linkuse as main transcript	c.1302T>C	p.Ile434=	synonymous_variant	11/17	ENST00000265362.9	NP_006071.1
SEMA3A	XM_005250110.4 linkuse as main transcript	c.1302T>C	p.Ile434=	synonymous_variant	14/20		XP_005250167.1
SEMA3A	XM_047419751.1 linkuse as main transcript	c.1302T>C	p.Ile434=	synonymous_variant	15/21		XP_047275707.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SEMA3A	ENST00000265362.9 linkuse as main transcript	c.1302T>C	p.Ile434=	synonymous_variant	11/17	1	NM_006080.3	ENSP00000265362	P1
SEMA3A	ENST00000436949.5 linkuse as main transcript	c.1302T>C	p.Ile434=	synonymous_variant	12/18	5		ENSP00000415260	P1

Frequencies

GnomAD3 genomes

AF:

0.243

AC:

36905

AN:

151844

Hom.:

4646

Cov.:

show subpopulations

Gnomad AFR

AF:

0.268

Gnomad AMI

AF:

0.248

Gnomad AMR

AF:

0.205

Gnomad ASJ

AF:

0.250

Gnomad EAS

AF:

0.163

Gnomad SAS

AF:

0.313

Gnomad FIN

AF:

0.301

Gnomad MID

AF:

0.309

Gnomad NFE

AF:

0.228

Gnomad OTH

AF:

0.236

GnomAD3 exomes

AF:

0.238

AC:

59845

AN:

251304

Hom.:

7563

AF XY:

0.246

AC XY:

33350

AN XY:

135814

show subpopulations

Gnomad AFR exome

AF:

0.267

Gnomad AMR exome

AF:

0.172

Gnomad ASJ exome

AF:

0.241

Gnomad EAS exome

AF:

0.150

Gnomad SAS exome

AF:

0.320

Gnomad FIN exome

AF:

0.306

Gnomad NFE exome

AF:

0.233

Gnomad OTH exome

AF:

0.240

GnomAD4 exome

AF:

0.230

AC:

336028

AN:

1460268

Hom.:

39768

Cov.:

AF XY:

0.233

AC XY:

169381

AN XY:

726532

show subpopulations

Gnomad4 AFR exome

AF:

0.265

Gnomad4 AMR exome

AF:

0.175

Gnomad4 ASJ exome

AF:

0.244

Gnomad4 EAS exome

AF:

0.166

Gnomad4 SAS exome

AF:

0.319

Gnomad4 FIN exome

AF:

0.303

Gnomad4 NFE exome

AF:

0.222

Gnomad4 OTH exome

AF:

0.237

GnomAD4 genome

AF:

0.243

AC:

36921

AN:

151962

Hom.:

4649

Cov.:

AF XY:

0.247

AC XY:

18329

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.268

Gnomad4 AMR

AF:

0.204

Gnomad4 ASJ

AF:

0.250

Gnomad4 EAS

AF:

0.163

Gnomad4 SAS

AF:

0.314

Gnomad4 FIN

AF:

0.301

Gnomad4 NFE

AF:

0.228

Gnomad4 OTH

AF:

0.235

Alfa

AF:

0.225

Hom.:

5946

Bravo

AF:

0.235

Asia WGS

AF:

0.235

AC:

820

AN:

3478

EpiCase

AF:

0.250

EpiControl

AF:

0.243

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 09, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

3.4

DANN

Benign

0.72

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

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