rs367686870
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_017417.2(GALNT8):c.625C>T(p.Pro209Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000322 in 1,613,736 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017417.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GALNT8 | ENST00000252318.7 | c.625C>T | p.Pro209Ser | missense_variant | Exon 3 of 11 | 1 | NM_017417.2 | ENSP00000252318.2 | ||
ENSG00000255639 | ENST00000648836.1 | c.964-21680C>T | intron_variant | Intron 10 of 14 | ENSP00000497305.1 | |||||
ENSG00000255639 | ENST00000544741.2 | n.*402C>T | non_coding_transcript_exon_variant | Exon 5 of 6 | 3 | ENSP00000456318.2 | ||||
ENSG00000255639 | ENST00000544741.2 | n.*402C>T | 3_prime_UTR_variant | Exon 5 of 6 | 3 | ENSP00000456318.2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251296Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135806
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461490Hom.: 0 Cov.: 30 AF XY: 0.0000344 AC XY: 25AN XY: 727052
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74444
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.625C>T (p.P209S) alteration is located in exon 3 (coding exon 3) of the GALNT8 gene. This alteration results from a C to T substitution at nucleotide position 625, causing the proline (P) at amino acid position 209 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