rs2116942
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_004230.4(S1PR2):c.919A>T(p.Arg307Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00012 in 1,609,182 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. R307R) has been classified as Benign.
Frequency
Consequence
NM_004230.4 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 |
---|---|---|---|---|---|---|---|
S1PR2 | NM_004230.4 | c.919A>T | p.Arg307Trp | missense_variant | 2/2 | ENST00000646641.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
S1PR2 | ENST00000646641.1 | c.919A>T | p.Arg307Trp | missense_variant | 2/2 | NM_004230.4 | P1 | ||
DNMT1 | ENST00000588952.5 | c.-401-5118A>T | intron_variant | 5 | |||||
DNMT1 | ENST00000592342.5 | c.-284+7217A>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000217 AC: 33AN: 151994Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000354 AC: 85AN: 239966Hom.: 1 AF XY: 0.000312 AC XY: 41AN XY: 131394
GnomAD4 exome AF: 0.000110 AC: 161AN: 1457070Hom.: 0 Cov.: 71 AF XY: 0.000121 AC XY: 88AN XY: 724374
GnomAD4 genome ? AF: 0.000210 AC: 32AN: 152112Hom.: 0 Cov.: 33 AF XY: 0.000269 AC XY: 20AN XY: 74360
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 07, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 06, 2020 | - - |
S1PR2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 05, 2022 | 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