chr8-50449698-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
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 (no stars).
Frequency
Consequence
NM_018967.5 missense
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SNTG1 | NM_018967.5 | c.250G>A | p.Val84Ile | missense_variant | Exon 6 of 19 | ENST00000642720.2 | NP_061840.1 |
Ensembl
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
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