chr2-154245966-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_052917.4(GALNT13):āc.841A>Gā(p.Arg281Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,460,494 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R281I) has been classified as Uncertain significance.
Frequency
Consequence
NM_052917.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALNT13 | NM_052917.4 | c.841A>G | p.Arg281Gly | missense_variant | 7/13 | ENST00000392825.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALNT13 | ENST00000392825.8 | c.841A>G | p.Arg281Gly | missense_variant | 7/13 | 2 | NM_052917.4 | P1 | |
GALNT13 | ENST00000409237.5 | c.841A>G | p.Arg281Gly | missense_variant | 5/12 | 1 | |||
GALNT13 | ENST00000431076.5 | c.*661A>G | 3_prime_UTR_variant, NMD_transcript_variant | 5/9 | 1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250882Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135598
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460494Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 726620
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 12, 2023 | The c.841A>G (p.R281G) alteration is located in exon 7 (coding exon 5) of the GALNT13 gene. This alteration results from a A to G substitution at nucleotide position 841, causing the arginine (R) at amino acid position 281 to be replaced by a glycine (G). 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