2-96861765-G-A
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BS2
The NM_017789.5(SEMA4C):c.1573C>T(p.Arg525Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,613,586 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000029 ( 0 hom. )
Consequence
SEMA4C
NM_017789.5 missense
NM_017789.5 missense
Scores
1
6
12
Clinical Significance
Conservation
PhyloP100: 1.88
Genes affected
SEMA4C (HGNC:10731): (semaphorin 4C) Predicted to enable chemorepellent activity and semaphorin receptor binding activity. Involved in muscle cell differentiation and positive regulation of stress-activated MAPK cascade. Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, SEMA4C
BS2
?
High AC in GnomAd4 at 7 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA4C | NM_017789.5 | c.1573C>T | p.Arg525Cys | missense_variant | 13/15 | ENST00000305476.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA4C | ENST00000305476.10 | c.1573C>T | p.Arg525Cys | missense_variant | 13/15 | 1 | NM_017789.5 | P1 | |
SEMA4C | ENST00000467747.1 | n.1564C>T | non_coding_transcript_exon_variant | 1/3 | 2 | ||||
SEMA4C | ENST00000474420.1 | n.683C>T | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
SEMA4C | ENST00000482925.5 | n.1963C>T | non_coding_transcript_exon_variant | 11/13 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152232Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000518 AC: 13AN: 250878Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135652
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GnomAD4 exome AF: 0.0000287 AC: 42AN: 1461236Hom.: 0 Cov.: 31 AF XY: 0.0000261 AC XY: 19AN XY: 726914
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GnomAD4 genome ? AF: 0.0000459 AC: 7AN: 152350Hom.: 0 Cov.: 33 AF XY: 0.0000805 AC XY: 6AN XY: 74504
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 28, 2023 | The c.1573C>T (p.R525C) alteration is located in exon 13 (coding exon 12) of the SEMA4C gene. This alteration results from a C to T substitution at nucleotide position 1573, causing the arginine (R) at amino acid position 525 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Uncertain
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
D
Sift4G
Uncertain
T
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at