rs2239816
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000367723.8(SUCO):c.31T>C(p.Ser11Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 1,612,794 control chromosomes in the GnomAD database, including 50,697 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
ENST00000367723.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SUCO | NM_016227.4 | c.31T>C | p.Ser11Pro | missense_variant | 1/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SUCO | ENST00000367723.8 | c.31T>C | p.Ser11Pro | missense_variant | 1/23 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.234 AC: 35615AN: 152044Hom.: 4325 Cov.: 32
GnomAD3 exomes AF: 0.246 AC: 60309AN: 244896Hom.: 8012 AF XY: 0.255 AC XY: 33914AN XY: 132976
GnomAD4 exome AF: 0.248 AC: 361639AN: 1460632Hom.: 46364 Cov.: 34 AF XY: 0.252 AC XY: 183201AN XY: 726520
GnomAD4 genome ? AF: 0.234 AC: 35637AN: 152162Hom.: 4333 Cov.: 32 AF XY: 0.234 AC XY: 17409AN XY: 74404
ClinVar
Submissions by phenotype
SUCO-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 31, 2019 | This variant is classified as 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