2-96860925-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_017789.5(SEMA4C):c.2203G>A(p.Gly735Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000719 in 1,612,958 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEMA4C | NM_017789.5 | c.2203G>A | p.Gly735Ser | missense_variant | 15/15 | ENST00000305476.10 | NP_060259.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SEMA4C | ENST00000305476.10 | c.2203G>A | p.Gly735Ser | missense_variant | 15/15 | 1 | NM_017789.5 | ENSP00000306844.5 | ||
SEMA4C | ENST00000467747.1 | n.2194G>A | non_coding_transcript_exon_variant | 3/3 | 2 | |||||
SEMA4C | ENST00000474420.1 | n.1436G>A | non_coding_transcript_exon_variant | 2/2 | 2 | |||||
SEMA4C | ENST00000482925.5 | n.2593G>A | non_coding_transcript_exon_variant | 13/13 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000124 AC: 31AN: 249058Hom.: 0 AF XY: 0.000185 AC XY: 25AN XY: 135358
GnomAD4 exome AF: 0.0000760 AC: 111AN: 1460772Hom.: 2 Cov.: 31 AF XY: 0.000111 AC XY: 81AN XY: 726700
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152186Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 08, 2024 | The c.2203G>A (p.G735S) 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 2203, causing the glycine (G) at amino acid position 735 to be replaced by a serine (S). 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