chr16-12902249-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001145204.3(SHISA9):c.185A>G(p.Asp62Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,544,498 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001145204.3 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 |
---|---|---|---|---|---|---|---|
SHISA9 | NM_001145204.3 | c.185A>G | p.Asp62Gly | missense_variant | 1/5 | ENST00000558583.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHISA9 | ENST00000558583.3 | c.185A>G | p.Asp62Gly | missense_variant | 1/5 | 5 | NM_001145204.3 | P1 | |
SHISA9 | ENST00000423335.2 | c.185A>G | p.Asp62Gly | missense_variant | 1/2 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151832Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000282 AC: 4AN: 141738Hom.: 0 AF XY: 0.0000391 AC XY: 3AN XY: 76646
GnomAD4 exome AF: 0.0000136 AC: 19AN: 1392552Hom.: 0 Cov.: 32 AF XY: 0.0000175 AC XY: 12AN XY: 687048
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151946Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74270
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 09, 2023 | The c.185A>G (p.D62G) alteration is located in exon 1 (coding exon 1) of the SHISA9 gene. This alteration results from a A to G substitution at nucleotide position 185, causing the aspartic acid (D) at amino acid position 62 to be replaced by a glycine (G). 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