8-50502773-T-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_018967.5(SNTG1):c.364-5T>C 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 0.00039 in 1,608,428 control chromosomes in the GnomAD database, including 2 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 Likely benign (no stars).
Frequency
Consequence
NM_018967.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SNTG1 | NM_018967.5 | c.364-5T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000642720.2 | NP_061840.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SNTG1 | ENST00000642720.2 | c.364-5T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_018967.5 | ENSP00000493900 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00205 AC: 312AN: 152218Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.000735 AC: 183AN: 248850Hom.: 1 AF XY: 0.000527 AC XY: 71AN XY: 134700
GnomAD4 exome AF: 0.000217 AC: 316AN: 1456092Hom.: 0 Cov.: 29 AF XY: 0.000195 AC XY: 141AN XY: 724730
GnomAD4 genome AF: 0.00204 AC: 311AN: 152336Hom.: 2 Cov.: 33 AF XY: 0.00184 AC XY: 137AN XY: 74492
ClinVar
Submissions by phenotype
SNTG1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 27, 2024 | 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