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GeneBe

1-151134828-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_030913.6(SEMA6C):c.1628G>C(p.Arg543Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00398 in 1,614,184 control chromosomes in the GnomAD database, including 218 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.021 ( 102 hom., cov: 32)
Exomes 𝑓: 0.0022 ( 116 hom. )

Consequence

SEMA6C
NM_030913.6 missense

Scores

2
15

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0370
Variant links:
Genes affected
SEMA6C (HGNC:10740): (semaphorin 6C) This gene encodes a member of the semaphorin family. Semaphorins represent important molecular signals controlling multiple aspects of the cellular response that follows CNS injury, and thus may play an important role in neural regeneration. [provided by RefSeq, May 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0017738342).
BP6
Variant 1-151134828-C-G is Benign according to our data. Variant chr1-151134828-C-G is described in ClinVar as [Benign]. Clinvar id is 767698.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0703 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SEMA6CNM_030913.6 linkuse as main transcriptc.1628G>C p.Arg543Thr missense_variant 16/19 ENST00000368914.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SEMA6CENST00000368914.8 linkuse as main transcriptc.1628G>C p.Arg543Thr missense_variant 16/191 NM_030913.6 P4Q9H3T2-1

Frequencies

GnomAD3 genomes
AF:
0.0210
AC:
3200
AN:
152200
Hom.:
102
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0725
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00994
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000176
Gnomad OTH
AF:
0.0143
GnomAD3 exomes
AF:
0.00565
AC:
1421
AN:
251472
Hom.:
60
AF XY:
0.00411
AC XY:
559
AN XY:
135908
show subpopulations
Gnomad AFR exome
AF:
0.0779
Gnomad AMR exome
AF:
0.00341
Gnomad ASJ exome
AF:
0.0000992
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000653
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000193
Gnomad OTH exome
AF:
0.00195
GnomAD4 exome
AF:
0.00219
AC:
3208
AN:
1461866
Hom.:
116
Cov.:
32
AF XY:
0.00189
AC XY:
1371
AN XY:
727238
show subpopulations
Gnomad4 AFR exome
AF:
0.0772
Gnomad4 AMR exome
AF:
0.00385
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000174
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000129
Gnomad4 OTH exome
AF:
0.00449
GnomAD4 genome
AF:
0.0211
AC:
3209
AN:
152318
Hom.:
102
Cov.:
32
AF XY:
0.0207
AC XY:
1542
AN XY:
74482
show subpopulations
Gnomad4 AFR
AF:
0.0725
Gnomad4 AMR
AF:
0.00993
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000176
Gnomad4 OTH
AF:
0.0142
Alfa
AF:
0.00160
Hom.:
5
Bravo
AF:
0.0242
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.000778
AC:
3
ESP6500AA
AF:
0.0794
AC:
350
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.00703
AC:
854
Asia WGS
AF:
0.00491
AC:
17
AN:
3478
EpiCase
AF:
0.000382
EpiControl
AF:
0.000178

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeMay 21, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Benign
-0.58
T
BayesDel_noAF
Benign
-0.54
Cadd
Benign
15
Dann
Benign
0.96
Eigen
Benign
-0.37
Eigen_PC
Benign
-0.33
FATHMM_MKL
Benign
0.23
N
LIST_S2
Benign
0.82
T;T;.;D
MetaRNN
Benign
0.0018
T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Uncertain
2.0
M;.;M;M
MutationTaster
Benign
0.95
N;N;N;N
PrimateAI
Benign
0.33
T
PROVEAN
Benign
-1.1
N;N;N;N
REVEL
Benign
0.024
Sift
Benign
0.12
T;T;T;T
Sift4G
Uncertain
0.035
D;D;D;D
Polyphen
0.013
B;B;B;B
Vest4
0.50
MVP
0.66
MPC
0.97
ClinPred
0.015
T
GERP RS
2.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0
Varity_R
0.087
gMVP
0.47

Splicing

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: rs74127528; hg19: chr1-151107304; API