chr3-16175465-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_054110.5(GALNT15):c.314G>A(p.Arg105Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000409 in 1,613,986 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_054110.5 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GALNT15 | NM_054110.5 | c.314G>A | p.Arg105Lys | missense_variant | 1/10 | ENST00000339732.10 | NP_473451.3 | |
GALNT15 | NM_001319051.2 | c.314G>A | p.Arg105Lys | missense_variant | 1/10 | NP_001305980.1 | ||
GALNT15 | XM_005264852.6 | c.314G>A | p.Arg105Lys | missense_variant | 1/10 | XP_005264909.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GALNT15 | ENST00000339732.10 | c.314G>A | p.Arg105Lys | missense_variant | 1/10 | 1 | NM_054110.5 | ENSP00000344260.5 | ||
GALNT15 | ENST00000437509.3 | c.314G>A | p.Arg105Lys | missense_variant | 1/10 | 1 | ENSP00000395873.1 | |||
GALNT15 | ENST00000470031.1 | n.49G>A | non_coding_transcript_exon_variant | 1/2 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251034Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135734
GnomAD4 exome AF: 0.0000410 AC: 60AN: 1461808Hom.: 0 Cov.: 31 AF XY: 0.0000468 AC XY: 34AN XY: 727192
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 19, 2022 | The c.314G>A (p.R105K) alteration is located in exon 1 (coding exon 1) of the GALNT15 gene. This alteration results from a G to A substitution at nucleotide position 314, causing the arginine (R) at amino acid position 105 to be replaced by a lysine (K). 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