9-34647868-G-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_000155.4(GALT):c.414G>T(p.Thr138=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000305 in 1,614,174 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T138T) has been classified as Likely benign.
Frequency
Consequence
NM_000155.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GALT | NM_000155.4 | c.414G>T | p.Thr138= | synonymous_variant | 5/11 | ENST00000378842.8 | |
GALT | NM_001258332.2 | c.87G>T | p.Thr29= | synonymous_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALT | ENST00000378842.8 | c.414G>T | p.Thr138= | synonymous_variant | 5/11 | 1 | NM_000155.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00156 AC: 238AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000426 AC: 107AN: 251444Hom.: 0 AF XY: 0.000346 AC XY: 47AN XY: 135898
GnomAD4 exome AF: 0.000174 AC: 254AN: 1461892Hom.: 0 Cov.: 33 AF XY: 0.000138 AC XY: 100AN XY: 727246
GnomAD4 genome ? AF: 0.00156 AC: 238AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.00157 AC XY: 117AN XY: 74476
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Sep 25, 2015 | - - |
GALT-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 02, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Galactosemia Benign:1
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | May 22, 2018 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Feb 01, 2017 | Variant summary: The GALT c.414G>T (p.Thr138Thr) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. Mutation taster predicts a damaging outcome for this variant, while 1/5 splice prediction tools predict the variant to create a splice donor site. Additionally, ESE finder predicts the creation of SRp40 binding site. However, these predictions are yet to be confirmed by functional studies. This variant was found in 66/121340 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.006255 (65/10392). This frequency is about 2 times the estimated maximal expected allele frequency of a pathogenic GALT variant (0.0028868), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. In addition, one clinical diagnostic laboratory classified this variant as benign. Taken together, this variant is classified as likely benign. - |
Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at