12-4720742-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017417.2(GALNT8):āc.65A>Gā(p.Asn22Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,613,676 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_017417.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GALNT8 | ENST00000252318.7 | c.65A>G | p.Asn22Ser | missense_variant | Exon 1 of 11 | 1 | NM_017417.2 | ENSP00000252318.2 | ||
ENSG00000255639 | ENST00000648836.1 | c.963+35417A>G | intron_variant | Intron 10 of 14 | ENSP00000497305.1 | |||||
ENSG00000255639 | ENST00000543979.1 | n.590-5790A>G | intron_variant | Intron 5 of 5 | 2 | |||||
ENSG00000255639 | ENST00000544741.2 | n.241-5790A>G | intron_variant | Intron 3 of 5 | 3 | ENSP00000456318.2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251398Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135866
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461502Hom.: 1 Cov.: 29 AF XY: 0.0000206 AC XY: 15AN XY: 727100
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.65A>G (p.N22S) alteration is located in exon 1 (coding exon 1) of the GALNT8 gene. This alteration results from a A to G substitution at nucleotide position 65, causing the asparagine (N) at amino acid position 22 to be replaced by a serine (S). 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