rs112682152
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001244710.2(GFPT1):c.408+7A>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00218 in 1,502,278 control chromosomes in the GnomAD database, including 62 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001244710.2 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GFPT1 | NM_001244710.2 | c.408+7A>T | splice_region_variant, intron_variant | ENST00000357308.9 | NP_001231639.1 | |||
GFPT1 | NM_002056.4 | c.408+7A>T | splice_region_variant, intron_variant | NP_002047.2 | ||||
GFPT1 | XM_017003801.2 | c.483+7A>T | splice_region_variant, intron_variant | XP_016859290.1 | ||||
GFPT1 | XM_017003802.3 | c.483+7A>T | splice_region_variant, intron_variant | XP_016859291.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GFPT1 | ENST00000357308.9 | c.408+7A>T | splice_region_variant, intron_variant | 5 | NM_001244710.2 | ENSP00000349860 | ||||
GFPT1 | ENST00000361060.5 | c.408+7A>T | splice_region_variant, intron_variant | 1 | ENSP00000354347 | P1 | ||||
GFPT1 | ENST00000674438.1 | c.192+7A>T | splice_region_variant, intron_variant | ENSP00000501469 | ||||||
GFPT1 | ENST00000674507.1 | c.408+7A>T | splice_region_variant, intron_variant | ENSP00000501332 |
Frequencies
GnomAD3 genomes AF: 0.0114 AC: 1731AN: 152170Hom.: 29 Cov.: 32
GnomAD3 exomes AF: 0.00309 AC: 775AN: 251144Hom.: 13 AF XY: 0.00224 AC XY: 304AN XY: 135738
GnomAD4 exome AF: 0.00114 AC: 1543AN: 1349990Hom.: 32 Cov.: 21 AF XY: 0.000949 AC XY: 643AN XY: 677872
GnomAD4 genome AF: 0.0114 AC: 1737AN: 152288Hom.: 30 Cov.: 32 AF XY: 0.0107 AC XY: 799AN XY: 74464
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Nov 07, 2017 | - - |
Congenital myasthenic syndrome 12 Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at