chr2-222424787-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001320833.2(SGPP2):c.-343C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000716 in 1,396,224 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001320833.2 5_prime_UTR_premature_start_codon_gain
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SGPP2 | NM_152386.4 | c.185C>T | p.Pro62Leu | missense_variant | Exon 1 of 5 | ENST00000321276.8 | NP_689599.2 | |
SGPP2 | NM_001320833.2 | c.-343C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 6 | NP_001307762.1 | |||
SGPP2 | NM_001320833.2 | c.-343C>T | 5_prime_UTR_variant | Exon 1 of 6 | NP_001307762.1 | |||
SGPP2 | NM_001320834.2 | c.-166+709C>T | intron_variant | Intron 1 of 4 | NP_001307763.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152022Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000470 AC: 2AN: 42534Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 25296
GnomAD4 exome AF: 0.0000772 AC: 96AN: 1244094Hom.: 1 Cov.: 30 AF XY: 0.0000871 AC XY: 53AN XY: 608816
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.185C>T (p.P62L) alteration is located in exon 1 (coding exon 1) of the SGPP2 gene. This alteration results from a C to T substitution at nucleotide position 185, causing the proline (P) at amino acid position 62 to be replaced by a leucine (L). 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