22-41910537-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001207020.3(SHISA8):āc.682A>Cā(p.Asn228His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000622 in 1,238,214 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHISA8 | NM_001207020.3 | c.682A>C | p.Asn228His | missense_variant | 3/4 | ENST00000621082.2 | |
SHISA8 | NM_001353438.2 | c.967A>C | p.Asn323His | missense_variant | 3/4 | ||
SHISA8 | NM_001353439.2 | c.859A>C | p.Asn287His | missense_variant | 3/4 | ||
SHISA8 | XM_006724256.5 | c.847A>C | p.Asn283His | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHISA8 | ENST00000621082.2 | c.682A>C | p.Asn228His | missense_variant | 3/4 | 5 | NM_001207020.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000660 AC: 10AN: 151626Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000617 AC: 67AN: 1086588Hom.: 0 Cov.: 31 AF XY: 0.0000619 AC XY: 32AN XY: 516966
GnomAD4 genome AF: 0.0000660 AC: 10AN: 151626Hom.: 0 Cov.: 32 AF XY: 0.0000811 AC XY: 6AN XY: 74028
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2024 | The c.682A>C (p.N228H) alteration is located in exon 3 (coding exon 3) of the SHISA8 gene. This alteration results from a A to C substitution at nucleotide position 682, causing the asparagine (N) at amino acid position 228 to be replaced by a histidine (H). 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