NM_001384900.1:c.2151C>A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_001384900.1(SEMA3D):c.2151C>A(p.Ile717Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,852 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
SEMA3D
NM_001384900.1 synonymous
NM_001384900.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.27
Publications
1 publications found
Genes affected
SEMA3D (HGNC:10726): (semaphorin 3D) This gene encodes a member of the semaphorin III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin like domain and a C-terminal basic domain. The protein encoded by this gene binds neuropilin and plays an important role in cardiovascular development. [provided by RefSeq, Aug 2016]
SEMA3D Gene-Disease associations (from GenCC):
- skeletal dysplasiaInheritance: AD Classification: LIMITED Submitted by: PanelApp Australia
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
Variant 7-84999623-G-T is Benign according to our data. Variant chr7-84999623-G-T is described in ClinVar as Likely_benign. ClinVar VariationId is 3029219.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=1.27 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001384900.1. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SEMA3D | MANE Select | c.2151C>A | p.Ile717Ile | synonymous | Exon 19 of 19 | NP_001371829.1 | O95025 | ||
| SEMA3D | c.2151C>A | p.Ile717Ile | synonymous | Exon 20 of 20 | NP_001371830.1 | O95025 | |||
| SEMA3D | c.2151C>A | p.Ile717Ile | synonymous | Exon 21 of 21 | NP_001371831.1 | O95025 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SEMA3D | TSL:5 MANE Select | c.2151C>A | p.Ile717Ile | synonymous | Exon 19 of 19 | ENSP00000284136.6 | O95025 | ||
| SEMA3D | TSL:1 | n.1277C>A | non_coding_transcript_exon | Exon 10 of 10 | |||||
| SEMA3D | c.2151C>A | p.Ile717Ile | synonymous | Exon 18 of 18 | ENSP00000586382.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00000398 AC: 1AN: 251426 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
251426
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461852Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727228 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1461852
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
727228
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33476
American (AMR)
AF:
AC:
0
AN:
44704
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26134
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
0
AN:
86256
European-Finnish (FIN)
AF:
AC:
0
AN:
53420
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1112002
Other (OTH)
AF:
AC:
0
AN:
60392
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
Bravo
AF:
EpiCase
AF:
EpiControl
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:no assertion criteria provided
Pathogenic
VUS
Benign
Condition
-
-
1
SEMA3D-related disorder (1)
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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