19-1108467-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014963.3(SBNO2):c.3854G>T(p.Gly1285Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000075 in 1,226,838 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G1285D) has been classified as Uncertain significance.
Frequency
Consequence
NM_014963.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SBNO2 | NM_014963.3 | c.3854G>T | p.Gly1285Val | missense_variant | 32/32 | ENST00000361757.8 | |
SBNO2 | NM_001100122.2 | c.3683G>T | p.Gly1228Val | missense_variant | 29/29 | ||
SBNO2 | XM_047438466.1 | c.2657G>T | p.Gly886Val | missense_variant | 29/29 | ||
SBNO2 | XM_011527804.4 | c.*184G>T | 3_prime_UTR_variant | 32/32 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SBNO2 | ENST00000361757.8 | c.3854G>T | p.Gly1285Val | missense_variant | 32/32 | 1 | NM_014963.3 | P2 | |
SBNO2 | ENST00000587024.5 | c.3824G>T | p.Gly1275Val | missense_variant | 32/32 | 2 | A2 | ||
SBNO2 | ENST00000438103.6 | c.3683G>T | p.Gly1228Val | missense_variant | 29/29 | 2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000127 AC: 19AN: 149532Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000678 AC: 73AN: 1077200Hom.: 1 Cov.: 33 AF XY: 0.0000716 AC XY: 37AN XY: 516436
GnomAD4 genome AF: 0.000127 AC: 19AN: 149638Hom.: 0 Cov.: 33 AF XY: 0.000178 AC XY: 13AN XY: 73066
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 13, 2022 | The c.3854G>T (p.G1285V) alteration is located in exon 32 (coding exon 31) of the SBNO2 gene. This alteration results from a G to T substitution at nucleotide position 3854, causing the glycine (G) at amino acid position 1285 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at