rs1357813

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000265362.9(SEMA3A):​c.547+442A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,096 control chromosomes in the GnomAD database, including 6,620 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 0.29 ( 6620 hom., cov: 33)

Consequence

SEMA3A
ENST00000265362.9 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.975
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SEMA3ANM_006080.3 linkuse as main transcriptc.547+442A>T intron_variant ENST00000265362.9 NP_006071.1
SEMA3AXM_005250110.4 linkuse as main transcriptc.547+442A>T intron_variant XP_005250167.1
SEMA3AXM_047419751.1 linkuse as main transcriptc.547+442A>T intron_variant XP_047275707.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SEMA3AENST00000265362.9 linkuse as main transcriptc.547+442A>T intron_variant 1 NM_006080.3 ENSP00000265362 P1
SEMA3AENST00000436949.5 linkuse as main transcriptc.547+442A>T intron_variant 5 ENSP00000415260 P1

Frequencies

GnomAD3 genomes
AF:
0.285
AC:
43316
AN:
151980
Hom.:
6613
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.391
Gnomad AMI
AF:
0.257
Gnomad AMR
AF:
0.284
Gnomad ASJ
AF:
0.289
Gnomad EAS
AF:
0.140
Gnomad SAS
AF:
0.353
Gnomad FIN
AF:
0.225
Gnomad MID
AF:
0.288
Gnomad NFE
AF:
0.237
Gnomad OTH
AF:
0.276
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.285
AC:
43360
AN:
152096
Hom.:
6620
Cov.:
33
AF XY:
0.287
AC XY:
21346
AN XY:
74356
show subpopulations
Gnomad4 AFR
AF:
0.391
Gnomad4 AMR
AF:
0.284
Gnomad4 ASJ
AF:
0.289
Gnomad4 EAS
AF:
0.140
Gnomad4 SAS
AF:
0.354
Gnomad4 FIN
AF:
0.225
Gnomad4 NFE
AF:
0.237
Gnomad4 OTH
AF:
0.275
Alfa
AF:
0.272
Hom.:
749
Bravo
AF:
0.292
Asia WGS
AF:
0.255
AC:
891
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.24
DANN
Benign
0.55

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.

Other links and lift over

dbSNP: rs1357813; hg19: chr7-83689339; API