12-20721830-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017435.5(SLCO1C1):c.802C>T(p.Pro268Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,614,022 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017435.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLCO1C1 | NM_017435.5 | c.802C>T | p.Pro268Ser | missense_variant | 8/15 | ENST00000266509.7 | |
SLCO1C1 | NM_001145946.2 | c.802C>T | p.Pro268Ser | missense_variant | 9/16 | ||
SLCO1C1 | NM_001145945.2 | c.655C>T | p.Pro219Ser | missense_variant | 8/15 | ||
SLCO1C1 | NM_001145944.2 | c.448C>T | p.Pro150Ser | missense_variant | 6/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO1C1 | ENST00000266509.7 | c.802C>T | p.Pro268Ser | missense_variant | 8/15 | 1 | NM_017435.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251398Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135878
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461840Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727218
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 09, 2021 | The c.802C>T (p.P268S) alteration is located in exon 9 (coding exon 7) of the SLCO1C1 gene. This alteration results from a C to T substitution at nucleotide position 802, causing the proline (P) at amino acid position 268 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at