2-157258674-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014568.3(GALNT5):c.592C>T(p.Arg198Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,686 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★).
Frequency
Consequence
NM_014568.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALNT5 | NM_014568.3 | c.592C>T | p.Arg198Trp | missense_variant | 1/10 | ENST00000259056.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALNT5 | ENST00000259056.5 | c.592C>T | p.Arg198Trp | missense_variant | 1/10 | 1 | NM_014568.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 151858Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000480 AC: 12AN: 249812Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135270
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461710Hom.: 0 Cov.: 33 AF XY: 0.0000206 AC XY: 15AN XY: 727162
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 151976Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 12, 2021 | The c.592C>T (p.R198W) alteration is located in exon 1 (coding exon 1) of the GALNT5 gene. This alteration results from a C to T substitution at nucleotide position 592, causing the arginine (R) at amino acid position 198 to be replaced by a tryptophan (W). 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