12-89523450-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003774.5(GALNT4):c.1100G>A(p.Arg367Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000682 in 1,613,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003774.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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 |
---|---|---|---|---|---|---|---|---|---|---|
GALNT4 | ENST00000529983.3 | c.1100G>A | p.Arg367Gln | missense_variant | Exon 1 of 1 | 6 | NM_003774.5 | ENSP00000436604.2 | ||
POC1B-GALNT4 | ENST00000548729.5 | c.1091G>A | p.Arg364Gln | missense_variant | Exon 3 of 3 | 2 | ENSP00000447852.1 | |||
POC1B | ENST00000313546.8 | c.100+1670G>A | intron_variant | Intron 2 of 11 | 1 | NM_172240.3 | ENSP00000323302.3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249294Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135268
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461746Hom.: 0 Cov.: 87 AF XY: 0.00000413 AC XY: 3AN XY: 727166
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1100G>A (p.R367Q) alteration is located in exon 1 (coding exon 1) of the GALNT4 gene. This alteration results from a G to A substitution at nucleotide position 1100, causing the arginine (R) at amino acid position 367 to be replaced by a glutamine (Q). 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