chr7-84002201-T-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006080.3(SEMA3A):c.1361-155A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,082 control chromosomes in the GnomAD database, including 4,306 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.23 ( 4306 hom., cov: 33)
Consequence
SEMA3A
NM_006080.3 intron
NM_006080.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0760
Publications
2 publications found
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 Gene-Disease associations (from GenCC):
- skeletal dysplasiaInheritance: AR Classification: DEFINITIVE Submitted by: G2P
- hypogonadotropic hypogonadism 16 with or without anosmiaInheritance: AD Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
- multiple congenital anomalies/dysmorphic syndromeInheritance: AR Classification: MODERATE Submitted by: Ambry Genetics
- Brugada syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Kallmann syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
Variant 7-84002201-T-C is Benign according to our data. Variant chr7-84002201-T-C is described in ClinVar as Benign. ClinVar VariationId is 1234621.Status of the report is criteria_provided_single_submitter, 1 stars.
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEMA3A | NM_006080.3 | c.1361-155A>G | intron_variant | Intron 11 of 16 | ENST00000265362.9 | NP_006071.1 | ||
SEMA3A | XM_005250110.4 | c.1361-155A>G | intron_variant | Intron 14 of 19 | XP_005250167.1 | |||
SEMA3A | XM_047419751.1 | c.1361-155A>G | intron_variant | Intron 15 of 20 | XP_047275707.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.235 AC: 35661AN: 151964Hom.: 4307 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
35661
AN:
151964
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.235 AC: 35670AN: 152082Hom.: 4306 Cov.: 33 AF XY: 0.238 AC XY: 17726AN XY: 74346 show subpopulations
GnomAD4 genome
AF:
AC:
35670
AN:
152082
Hom.:
Cov.:
33
AF XY:
AC XY:
17726
AN XY:
74346
show subpopulations
African (AFR)
AF:
AC:
9902
AN:
41484
American (AMR)
AF:
AC:
3082
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
AC:
868
AN:
3468
East Asian (EAS)
AF:
AC:
839
AN:
5176
South Asian (SAS)
AF:
AC:
1513
AN:
4822
European-Finnish (FIN)
AF:
AC:
3172
AN:
10550
Middle Eastern (MID)
AF:
AC:
87
AN:
294
European-Non Finnish (NFE)
AF:
AC:
15503
AN:
67996
Other (OTH)
AF:
AC:
478
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
1403
2806
4208
5611
7014
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
384
768
1152
1536
1920
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
811
AN:
3476
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Aug 09, 2018
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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