chr14-69260417-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001168368.2(GALNT16):c.127G>T(p.Ala43Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000939 in 1,597,946 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001168368.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALNT16 | NM_001168368.2 | c.127G>T | p.Ala43Ser | missense_variant | 1/15 | ENST00000448469.8 | |
GALNT16-AS1 | NR_184249.1 | n.111C>A | non_coding_transcript_exon_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALNT16 | ENST00000448469.8 | c.127G>T | p.Ala43Ser | missense_variant | 1/15 | 1 | NM_001168368.2 | P1 | |
ENST00000556316.1 | n.151C>A | non_coding_transcript_exon_variant | 1/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151910Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000136 AC: 3AN: 219802Hom.: 0 AF XY: 0.0000168 AC XY: 2AN XY: 119312
GnomAD4 exome AF: 0.00000830 AC: 12AN: 1446036Hom.: 0 Cov.: 32 AF XY: 0.0000111 AC XY: 8AN XY: 718030
GnomAD4 genome AF: 0.0000197 AC: 3AN: 151910Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2AN XY: 74176
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2023 | The c.127G>T (p.A43S) alteration is located in exon 1 (coding exon 1) of the GALNT16 gene. This alteration results from a G to T substitution at nucleotide position 127, causing the alanine (A) at amino acid position 43 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