rs17374298
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The ENST00000558014.5(SEMA6D):c.-87+31736G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,146 control chromosomes in the GnomAD database, including 2,543 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 0.16 ( 2543 hom., cov: 32)
Consequence
SEMA6D
ENST00000558014.5 intron
ENST00000558014.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.74
Publications
0 publications found
Genes affected
SEMA6D (HGNC:16770): (semaphorin 6D) Semaphorins are a large family, including both secreted and membrane associated proteins, many of which have been implicated as inhibitors or chemorepellents in axon pathfinding, fasciculation and branching, and target selection. All semaphorins possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Additional sequence motifs C-terminal to the semaphorin domain allow classification into distinct subfamilies. Results demonstrate that transmembrane semaphorins, like the secreted ones, can act as repulsive axon guidance cues. This gene encodes a class 6 vertebrate transmembrane semaphorin that demonstrates alternative splicing. Several transcript variants have been identified and expression of the distinct encoded isoforms is thought to be regulated in a tissue- and development-dependent manner. [provided by RefSeq, Nov 2010]
SEMA6D Gene-Disease associations (from GenCC):
- complex neurodevelopmental disorderInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.28).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SEMA6D | ENST00000558014.5 | c.-87+31736G>C | intron_variant | Intron 3 of 19 | 1 | ENSP00000452815.1 | ||||
SEMA6D | ENST00000559184.5 | c.-87+31736G>C | intron_variant | Intron 4 of 5 | 4 | ENSP00000453097.1 | ||||
SEMA6D | ENST00000560636.5 | c.-171+31736G>C | intron_variant | Intron 3 of 5 | 4 | ENSP00000453420.1 |
Frequencies
GnomAD3 genomes AF: 0.160 AC: 24350AN: 152028Hom.: 2548 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
24350
AN:
152028
Hom.:
Cov.:
32
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: 0.160 AC: 24336AN: 152146Hom.: 2543 Cov.: 32 AF XY: 0.165 AC XY: 12256AN XY: 74366 show subpopulations
GnomAD4 genome
AF:
AC:
24336
AN:
152146
Hom.:
Cov.:
32
AF XY:
AC XY:
12256
AN XY:
74366
show subpopulations
African (AFR)
AF:
AC:
1636
AN:
41546
American (AMR)
AF:
AC:
1875
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
AC:
673
AN:
3468
East Asian (EAS)
AF:
AC:
245
AN:
5166
South Asian (SAS)
AF:
AC:
1329
AN:
4820
European-Finnish (FIN)
AF:
AC:
3034
AN:
10546
Middle Eastern (MID)
AF:
AC:
42
AN:
294
European-Non Finnish (NFE)
AF:
AC:
14937
AN:
68000
Other (OTH)
AF:
AC:
347
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1007
2013
3020
4026
5033
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
284
568
852
1136
1420
<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:
450
AN:
3474
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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