1-151132921-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_030913.6(SEMA6C):c.2356C>T(p.Pro786Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000807 in 1,238,882 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_030913.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA6C | NM_030913.6 | c.2356C>T | p.Pro786Ser | missense_variant | 19/19 | ENST00000368914.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA6C | ENST00000368914.8 | c.2356C>T | p.Pro786Ser | missense_variant | 19/19 | 1 | NM_030913.6 | P4 | |
SEMA6C | ENST00000368913.7 | c.2452C>T | p.Pro818Ser | missense_variant | 20/20 | 1 | A1 | ||
SEMA6C | ENST00000341697.7 | c.2356C>T | p.Pro786Ser | missense_variant | 19/19 | 1 | P4 | ||
SEMA6C | ENST00000368912.7 | c.2332C>T | p.Pro778Ser | missense_variant | 19/19 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 8.07e-7 AC: 1AN: 1238882Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 612326
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.2452C>T (p.P818S) alteration is located in exon 20 (coding exon 18) of the SEMA6C gene. This alteration results from a C to T substitution at nucleotide position 2452, causing the proline (P) at amino acid position 818 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