rs190148089
Variant summary
Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_003781.4(B3GALNT1):c.-237T>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00144 in 1,289,766 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_003781.4 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -9 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| B3GALNT1 | NM_003781.4 | c.-237T>G | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 5 | ENST00000320474.10 | NP_003772.1 | ||
| B3GALNT1 | NM_003781.4 | c.-237T>G | 5_prime_UTR_variant | Exon 2 of 5 | ENST00000320474.10 | NP_003772.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| B3GALNT1 | ENST00000320474.10 | c.-237T>G | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 5 | 1 | NM_003781.4 | ENSP00000323479.4 | |||
| B3GALNT1 | ENST00000320474.10 | c.-237T>G | 5_prime_UTR_variant | Exon 2 of 5 | 1 | NM_003781.4 | ENSP00000323479.4 |
Frequencies
GnomAD3 genomes AF: 0.00122 AC: 186AN: 152202Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00131 AC: 179AN: 136878 AF XY: 0.00108 show subpopulations
GnomAD4 exome AF: 0.00147 AC: 1674AN: 1137446Hom.: 3 Cov.: 30 AF XY: 0.00144 AC XY: 801AN XY: 558012 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00122 AC: 186AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.00132 AC XY: 98AN XY: 74476 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
B3GALNT1-related disorder Benign:1
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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at