chr8-133463467-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_173344.3(ST3GAL1):c.684-8A>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00784 in 1,613,740 control chromosomes in the GnomAD database, including 63 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_173344.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ST3GAL1 | NM_173344.3 | c.684-8A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000522652.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST3GAL1 | ENST00000522652.6 | c.684-8A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_173344.3 | P1 | |||
ST3GAL1 | ENST00000521180.5 | c.684-8A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | P1 | ||||
ST3GAL1 | ENST00000648219.1 | c.684-8A>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00632 AC: 962AN: 152116Hom.: 9 Cov.: 33
GnomAD3 exomes AF: 0.00718 AC: 1794AN: 249692Hom.: 14 AF XY: 0.00732 AC XY: 987AN XY: 134748
GnomAD4 exome AF: 0.00800 AC: 11689AN: 1461506Hom.: 54 Cov.: 31 AF XY: 0.00799 AC XY: 5809AN XY: 726998
GnomAD4 genome ? AF: 0.00632 AC: 962AN: 152234Hom.: 9 Cov.: 33 AF XY: 0.00627 AC XY: 467AN XY: 74428
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 04, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at