chr8-50449698-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_018967.5(SNTG1):c.250G>A(p.Val84Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00228 in 1,594,966 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_018967.5 missense
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 |
---|---|---|---|---|---|---|---|
SNTG1 | NM_018967.5 | c.250G>A | p.Val84Ile | missense_variant | 6/19 | ENST00000642720.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNTG1 | ENST00000642720.2 | c.250G>A | p.Val84Ile | missense_variant | 6/19 | NM_018967.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00136 AC: 207AN: 152062Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00136 AC: 335AN: 245820Hom.: 2 AF XY: 0.00151 AC XY: 201AN XY: 133012
GnomAD4 exome AF: 0.00238 AC: 3429AN: 1442786Hom.: 19 Cov.: 29 AF XY: 0.00237 AC XY: 1704AN XY: 717518
GnomAD4 genome ? AF: 0.00135 AC: 206AN: 152180Hom.: 0 Cov.: 33 AF XY: 0.00124 AC XY: 92AN XY: 74408
ClinVar
Submissions by phenotype
SNTG1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 10, 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at