19-10224657-G-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_004230.4(S1PR2):c.249C>G(p.Gly83=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G83G) has been classified as Benign.
Frequency
Consequence
NM_004230.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
S1PR2 | NM_004230.4 | c.249C>G | p.Gly83= | synonymous_variant | 2/2 | ENST00000646641.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
S1PR2 | ENST00000646641.1 | c.249C>G | p.Gly83= | synonymous_variant | 2/2 | NM_004230.4 | P1 | ||
DNMT1 | ENST00000588952.5 | c.-401-5788C>G | intron_variant | 5 | |||||
DNMT1 | ENST00000592342.5 | c.-284+6547C>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 248136Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134830
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000137 AC: 2AN: 1460980Hom.: 0 Cov.: 35 AF XY: 0.00000138 AC XY: 1AN XY: 726808
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at