22-41910053-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001207020.3(SHISA8):c.906G>C(p.Leu302Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000496 in 1,255,012 control chromosomes in the GnomAD database, including 1 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 (★).
Frequency
Consequence
NM_001207020.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SHISA8 | NM_001207020.3 | c.906G>C | p.Leu302Phe | missense_variant | Exon 4 of 4 | ENST00000621082.2 | NP_001193949.1 | |
SHISA8 | NM_001353438.2 | c.1191G>C | p.Leu397Phe | missense_variant | Exon 4 of 4 | NP_001340367.1 | ||
SHISA8 | NM_001353439.2 | c.1083G>C | p.Leu361Phe | missense_variant | Exon 4 of 4 | NP_001340368.1 | ||
SHISA8 | XM_006724256.5 | c.1071G>C | p.Leu357Phe | missense_variant | Exon 4 of 4 | XP_006724319.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000606 AC: 92AN: 151814Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.000480 AC: 530AN: 1103090Hom.: 1 Cov.: 31 AF XY: 0.000477 AC XY: 250AN XY: 523660
GnomAD4 genome AF: 0.000606 AC: 92AN: 151922Hom.: 0 Cov.: 33 AF XY: 0.000660 AC XY: 49AN XY: 74276
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.906G>C (p.L302F) alteration is located in exon 4 (coding exon 4) of the SHISA8 gene. This alteration results from a G to C substitution at nucleotide position 906, causing the leucine (L) at amino acid position 302 to be replaced by a phenylalanine (F). 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