chr15-75607263-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005701.4(SNUPN):c.553G>A(p.Val185Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000158 in 1,613,740 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_005701.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SNUPN | NM_005701.4 | c.553G>A | p.Val185Ile | missense_variant | 6/9 | ENST00000308588.10 | NP_005692.1 | |
SNUPN | NM_001042581.2 | c.553G>A | p.Val185Ile | missense_variant | 6/9 | NP_001036046.1 | ||
SNUPN | NM_001042588.2 | c.553G>A | p.Val185Ile | missense_variant | 6/9 | NP_001036053.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SNUPN | ENST00000308588.10 | c.553G>A | p.Val185Ile | missense_variant | 6/9 | 1 | NM_005701.4 | ENSP00000309831.5 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000155 AC: 39AN: 251184Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135746
GnomAD4 exome AF: 0.000157 AC: 230AN: 1461574Hom.: 0 Cov.: 30 AF XY: 0.000150 AC XY: 109AN XY: 727090
GnomAD4 genome AF: 0.000164 AC: 25AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2024 | The c.553G>A (p.V185I) alteration is located in exon 6 (coding exon 5) of the SNUPN gene. This alteration results from a G to A substitution at nucleotide position 553, causing the valine (V) at amino acid position 185 to be replaced by an isoleucine (I). 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