chr12-20715279-T-C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_017435.5(SLCO1C1):c.670T>C(p.Tyr224His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,712 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y224N) has been classified as Uncertain significance.
Frequency
Consequence
NM_017435.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLCO1C1 | NM_017435.5 | c.670T>C | p.Tyr224His | missense_variant | 6/15 | ENST00000266509.7 | |
SLCO1C1 | NM_001145946.2 | c.670T>C | p.Tyr224His | missense_variant | 7/16 | ||
SLCO1C1 | NM_001145944.2 | c.316T>C | p.Tyr106His | missense_variant | 4/13 | ||
SLCO1C1 | NM_001145945.2 | c.530-1853T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO1C1 | ENST00000266509.7 | c.670T>C | p.Tyr224His | missense_variant | 6/15 | 1 | NM_017435.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152252Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461460Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727002
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152252Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 26, 2023 | The c.670T>C (p.Y224H) alteration is located in exon 7 (coding exon 5) of the SLCO1C1 gene. This alteration results from a T to C substitution at nucleotide position 670, causing the tyrosine (Y) at amino acid position 224 to be replaced by a histidine (H). 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