12-20711503-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017435.5(SLCO1C1):c.522A>G(p.Ile174Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000992 in 1,613,464 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.522A>G | p.Ile174Met | missense_variant | 5/15 | ENST00000266509.7 | |
SLCO1C1 | NM_001145946.2 | c.522A>G | p.Ile174Met | missense_variant | 6/16 | ||
SLCO1C1 | NM_001145945.2 | c.522A>G | p.Ile174Met | missense_variant | 6/15 | ||
SLCO1C1 | NM_001145944.2 | c.168A>G | p.Ile56Met | missense_variant | 3/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO1C1 | ENST00000266509.7 | c.522A>G | p.Ile174Met | missense_variant | 5/15 | 1 | NM_017435.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250862Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135562
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461348Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 726960
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2022 | The c.522A>G (p.I174M) alteration is located in exon 6 (coding exon 4) of the SLCO1C1 gene. This alteration results from a A to G substitution at nucleotide position 522, causing the isoleucine (I) at amino acid position 174 to be replaced by a methionine (M). 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