17-11263505-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_207386.4(SHISA6):c.778C>T(p.Arg260Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000451 in 1,551,560 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R260H) has been classified as Uncertain significance.
Frequency
Consequence
NM_207386.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHISA6 | NM_207386.4 | c.778C>T | p.Arg260Cys | missense_variant | 2/6 | ENST00000441885.8 | |
SHISA6 | NM_001173462.2 | c.778C>T | p.Arg260Cys | missense_variant | 2/5 | ||
SHISA6 | NM_001173461.2 | c.778C>T | p.Arg260Cys | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHISA6 | ENST00000441885.8 | c.778C>T | p.Arg260Cys | missense_variant | 2/6 | 5 | NM_207386.4 | ||
SHISA6 | ENST00000432116.7 | c.778C>T | p.Arg260Cys | missense_variant | 2/5 | 1 | |||
SHISA6 | ENST00000409168.7 | c.778C>T | p.Arg260Cys | missense_variant | 2/4 | 1 | P1 | ||
SHISA6 | ENST00000343478.7 | c.262C>T | p.Arg88Cys | missense_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000255 AC: 4AN: 156690Hom.: 0 AF XY: 0.0000241 AC XY: 2AN XY: 83006
GnomAD4 exome AF: 0.0000479 AC: 67AN: 1399422Hom.: 0 Cov.: 31 AF XY: 0.0000435 AC XY: 30AN XY: 690216
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 18, 2023 | The c.778C>T (p.R260C) alteration is located in exon 2 (coding exon 2) of the SHISA6 gene. This alteration results from a C to T substitution at nucleotide position 778, causing the arginine (R) at amino acid position 260 to be replaced by a cysteine (C). 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