rs17763658
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_175882.3(SPPL2C):c.368G>A(p.Arg123Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0736 in 1,613,782 control chromosomes in the GnomAD database, including 4,597 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_175882.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0784 AC: 11934AN: 152126Hom.: 484 Cov.: 33
GnomAD3 exomes AF: 0.0798 AC: 20004AN: 250692Hom.: 812 AF XY: 0.0792 AC XY: 10742AN XY: 135604
GnomAD4 exome AF: 0.0731 AC: 106897AN: 1461538Hom.: 4110 Cov.: 30 AF XY: 0.0737 AC XY: 53578AN XY: 727088
GnomAD4 genome AF: 0.0785 AC: 11951AN: 152244Hom.: 487 Cov.: 33 AF XY: 0.0821 AC XY: 6107AN XY: 74430
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 15, 2020 | This variant is associated with the following publications: (PMID: 24166410) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at