NM_001244710.2:c.*22C>T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001244710.2(GFPT1):c.*22C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000265 in 1,511,468 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001244710.2 3_prime_UTR
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GFPT1 | NM_001244710.2 | c.*22C>T | 3_prime_UTR_variant | Exon 20 of 20 | ENST00000357308.9 | NP_001231639.1 | ||
GFPT1 | NM_002056.4 | c.*22C>T | 3_prime_UTR_variant | Exon 19 of 19 | NP_002047.2 | |||
GFPT1 | XM_017003801.2 | c.*22C>T | 3_prime_UTR_variant | Exon 20 of 20 | XP_016859290.1 | |||
GFPT1 | XM_017003802.3 | c.*22C>T | 3_prime_UTR_variant | Exon 19 of 19 | XP_016859291.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GFPT1 | ENST00000357308 | c.*22C>T | 3_prime_UTR_variant | Exon 20 of 20 | 5 | NM_001244710.2 | ENSP00000349860.4 | |||
GFPT1 | ENST00000361060 | c.*22C>T | 3_prime_UTR_variant | Exon 19 of 19 | 1 | ENSP00000354347.4 | ||||
GFPT1 | ENST00000674507 | c.*22C>T | 3_prime_UTR_variant | Exon 18 of 18 | ENSP00000501332.1 | |||||
GFPT1 | ENST00000674438 | c.*22C>T | 3_prime_UTR_variant | Exon 17 of 17 | ENSP00000501469.1 |
Frequencies
GnomAD3 genomes AF: 0.000113 AC: 17AN: 151010Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249944Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135082
GnomAD4 exome AF: 0.0000169 AC: 23AN: 1360342Hom.: 0 Cov.: 22 AF XY: 0.0000132 AC XY: 9AN XY: 682422
GnomAD4 genome AF: 0.000112 AC: 17AN: 151126Hom.: 0 Cov.: 32 AF XY: 0.0000950 AC XY: 7AN XY: 73708
ClinVar
Submissions by phenotype
Congenital myasthenic syndrome 12 Uncertain:1
This variant occurs in a non-coding region of the GFPT1 gene. It does not change the encoded amino acid sequence of the GFPT1 protein. This variant is present in population databases (rs199678034, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with GFPT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1505977). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at