chr22-41910096-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001207020.3(SHISA8):āc.863C>Gā(p.Pro288Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00561 in 1,239,556 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001207020.3 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 | UniProt |
---|---|---|---|---|---|---|---|
SHISA8 | NM_001207020.3 | c.863C>G | p.Pro288Arg | missense_variant | 4/4 | ENST00000621082.2 | |
SHISA8 | NM_001353438.2 | c.1148C>G | p.Pro383Arg | missense_variant | 4/4 | ||
SHISA8 | NM_001353439.2 | c.1040C>G | p.Pro347Arg | missense_variant | 4/4 | ||
SHISA8 | XM_006724256.5 | c.1028C>G | p.Pro343Arg | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHISA8 | ENST00000621082.2 | c.863C>G | p.Pro288Arg | missense_variant | 4/4 | 5 | NM_001207020.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00392 AC: 595AN: 151914Hom.: 4 Cov.: 33
GnomAD4 exome AF: 0.00584 AC: 6355AN: 1087534Hom.: 20 Cov.: 31 AF XY: 0.00585 AC XY: 3011AN XY: 514346
GnomAD4 genome AF: 0.00391 AC: 595AN: 152022Hom.: 4 Cov.: 33 AF XY: 0.00361 AC XY: 268AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 29, 2023 | The c.863C>G (p.P288R) alteration is located in exon 4 (coding exon 4) of the SHISA8 gene. This alteration results from a C to G substitution at nucleotide position 863, causing the proline (P) at amino acid position 288 to be replaced by an arginine (R). 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