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GeneBe

rs7779029

Variant summary

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

The NM_006379.5(SEMA3C):c.103+13883A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,134 control chromosomes in the GnomAD database, including 2,681 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 0.14 ( 2681 hom., cov: 32)

Consequence

SEMA3C
NM_006379.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.461
Variant links:
Genes affected
SEMA3C (HGNC:10725): (semaphorin 3C) This gene encodes a secreted glycoprotein that belongs to the semaphorin class 3 family of neuronal guidance cues. The encoded protein contains an N-terminal sema domain, integrin and immunoglobulin-like domains, and a C-terminal basic domain. Homodimerization and proteolytic cleavage of the C-terminal propeptide are necessary for the function of the encoded protein. It binds a neuropilin co-receptor before forming a heterotrimeric complex with an associated plexin. An increase in the expression of this gene correlates with an increase in cancer cell invasion and adhesion. Naturally occurring mutations in this gene are associated with Hirschsprung disease. [provided by RefSeq, May 2017]

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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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SEMA3CNM_006379.5 linkuse as main transcriptc.103+13883A>G intron_variant ENST00000265361.8
SEMA3CNM_001350120.2 linkuse as main transcriptc.157+13883A>G intron_variant
SEMA3CNM_001350121.2 linkuse as main transcriptc.-72+3033A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SEMA3CENST00000265361.8 linkuse as main transcriptc.103+13883A>G intron_variant 1 NM_006379.5 P1Q99985-1

Frequencies

GnomAD3 genomes
AF:
0.139
AC:
21167
AN:
152016
Hom.:
2655
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.333
Gnomad AMI
AF:
0.0285
Gnomad AMR
AF:
0.0908
Gnomad ASJ
AF:
0.133
Gnomad EAS
AF:
0.162
Gnomad SAS
AF:
0.109
Gnomad FIN
AF:
0.0140
Gnomad MID
AF:
0.142
Gnomad NFE
AF:
0.0542
Gnomad OTH
AF:
0.136
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.140
AC:
21246
AN:
152134
Hom.:
2681
Cov.:
32
AF XY:
0.135
AC XY:
10071
AN XY:
74376
show subpopulations
Gnomad4 AFR
AF:
0.334
Gnomad4 AMR
AF:
0.0907
Gnomad4 ASJ
AF:
0.133
Gnomad4 EAS
AF:
0.162
Gnomad4 SAS
AF:
0.110
Gnomad4 FIN
AF:
0.0140
Gnomad4 NFE
AF:
0.0542
Gnomad4 OTH
AF:
0.138
Alfa
AF:
0.0796
Hom.:
477
Bravo
AF:
0.152
Asia WGS
AF:
0.170
AC:
590
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
Cadd
Benign
0.55
Dann
Benign
0.37

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: rs7779029; hg19: chr7-80532112; API