chr2-96861062-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4_Moderate
The NM_017789.5(SEMA4C):c.2066G>A(p.Arg689Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,612,844 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017789.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA4C | NM_017789.5 | c.2066G>A | p.Arg689Gln | missense_variant | 15/15 | ENST00000305476.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA4C | ENST00000305476.10 | c.2066G>A | p.Arg689Gln | missense_variant | 15/15 | 1 | NM_017789.5 | P1 | |
SEMA4C | ENST00000467747.1 | n.2057G>A | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
SEMA4C | ENST00000474420.1 | n.1299G>A | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
SEMA4C | ENST00000482925.5 | n.2456G>A | non_coding_transcript_exon_variant | 13/13 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248274Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 135006
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460544Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726544
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152300Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2023 | The c.2066G>A (p.R689Q) alteration is located in exon 15 (coding exon 14) of the SEMA4C gene. This alteration results from a G to A substitution at nucleotide position 2066, causing the arginine (R) at amino acid position 689 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at