2-154245817-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_052917.4(GALNT13):c.692C>T(p.Thr231Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000347 in 1,586,428 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar 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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GALNT13 | ENST00000392825.8 | c.692C>T | p.Thr231Met | missense_variant | Exon 7 of 13 | 2 | NM_052917.4 | ENSP00000376570.3 | ||
GALNT13 | ENST00000409237.5 | c.692C>T | p.Thr231Met | missense_variant | Exon 5 of 12 | 1 | ENSP00000387239.1 | |||
GALNT13 | ENST00000431076.5 | n.*512C>T | non_coding_transcript_exon_variant | Exon 5 of 9 | 1 | ENSP00000389447.1 | ||||
GALNT13 | ENST00000431076.5 | n.*512C>T | 3_prime_UTR_variant | Exon 5 of 9 | 1 | ENSP00000389447.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000165 AC: 4AN: 242434Hom.: 0 AF XY: 0.00000764 AC XY: 1AN XY: 130962
GnomAD4 exome AF: 0.0000363 AC: 52AN: 1434340Hom.: 0 Cov.: 28 AF XY: 0.0000323 AC XY: 23AN XY: 711600
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.692C>T (p.T231M) alteration is located in exon 7 (coding exon 5) of the GALNT13 gene. This alteration results from a C to T substitution at nucleotide position 692, causing the threonine (T) at amino acid position 231 to be replaced by a methionine (M). 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