22-41909950-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001207020.3(SHISA8):c.1009G>A(p.Ala337Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000379 in 1,476,514 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 (★).
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHISA8 | NM_001207020.3 | c.1009G>A | p.Ala337Thr | missense_variant | 4/4 | ENST00000621082.2 | |
SHISA8 | NM_001353438.2 | c.1294G>A | p.Ala432Thr | missense_variant | 4/4 | ||
SHISA8 | NM_001353439.2 | c.1186G>A | p.Ala396Thr | missense_variant | 4/4 | ||
SHISA8 | XM_006724256.5 | c.1174G>A | p.Ala392Thr | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHISA8 | ENST00000621082.2 | c.1009G>A | p.Ala337Thr | missense_variant | 4/4 | 5 | NM_001207020.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152012Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000237 AC: 19AN: 80036Hom.: 0 AF XY: 0.000265 AC XY: 12AN XY: 45332
GnomAD4 exome AF: 0.0000385 AC: 51AN: 1324502Hom.: 0 Cov.: 31 AF XY: 0.0000445 AC XY: 29AN XY: 652038
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152012Hom.: 0 Cov.: 33 AF XY: 0.0000539 AC XY: 4AN XY: 74260
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2023 | The c.1009G>A (p.A337T) alteration is located in exon 4 (coding exon 4) of the SHISA8 gene. This alteration results from a G to A substitution at nucleotide position 1009, causing the alanine (A) at amino acid position 337 to be replaced by a threonine (T). 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