2-96860696-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_017789.5(SEMA4C):āc.2432A>Gā(p.Asp811Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,388 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_017789.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEMA4C | NM_017789.5 | c.2432A>G | p.Asp811Gly | 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.2432A>G | p.Asp811Gly | missense_variant | 15/15 | 1 | NM_017789.5 | ENSP00000306844.5 | ||
SEMA4C | ENST00000467747.1 | n.2423A>G | non_coding_transcript_exon_variant | 3/3 | 2 | |||||
SEMA4C | ENST00000474420.1 | n.1665A>G | non_coding_transcript_exon_variant | 2/2 | 2 | |||||
SEMA4C | ENST00000482925.5 | n.2822A>G | non_coding_transcript_exon_variant | 13/13 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250742Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135656
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461192Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726902
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 09, 2024 | The c.2432A>G (p.D811G) alteration is located in exon 15 (coding exon 14) of the SEMA4C gene. This alteration results from a A to G substitution at nucleotide position 2432, causing the aspartic acid (D) at amino acid position 811 to be replaced by a glycine (G). 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