chr19-10223987-T-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_004230.4(S1PR2):āc.919A>Cā(p.Arg307Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 1,608,656 control chromosomes in the GnomAD database, including 278,286 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_004230.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
S1PR2 | NM_004230.4 | c.919A>C | p.Arg307Arg | synonymous_variant | Exon 2 of 2 | ENST00000646641.1 | NP_004221.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
S1PR2 | ENST00000646641.1 | c.919A>C | p.Arg307Arg | synonymous_variant | Exon 2 of 2 | NM_004230.4 | ENSP00000496438.1 | |||
DNMT1 | ENST00000588952.5 | c.-401-5118A>C | intron_variant | Intron 1 of 8 | 5 | ENSP00000467050.1 | ||||
DNMT1 | ENST00000592342.5 | c.-284+7217A>C | intron_variant | Intron 1 of 6 | 3 | ENSP00000465993.1 |
Frequencies
GnomAD3 genomes AF: 0.603 AC: 91661AN: 151956Hom.: 28471 Cov.: 33
GnomAD3 exomes AF: 0.537 AC: 128942AN: 239966Hom.: 36064 AF XY: 0.542 AC XY: 71166AN XY: 131394
GnomAD4 exome AF: 0.581 AC: 845901AN: 1456582Hom.: 249795 Cov.: 71 AF XY: 0.579 AC XY: 419520AN XY: 724116
GnomAD4 genome AF: 0.603 AC: 91727AN: 152074Hom.: 28491 Cov.: 33 AF XY: 0.594 AC XY: 44172AN XY: 74338
ClinVar
Submissions by phenotype
not specified Benign:2
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
p.Arg307Arg in exon 2 of S1PR2: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, is not located withi n the splice consensus sequence, and has been identified in 73.32% (6474/8830) o f African chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.bro adinstitute.org; dbSNP rs2116942). -
not provided Benign:2
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Autosomal recessive nonsyndromic hearing loss 68 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at