12-20723234-C-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000266509.7(SLCO1C1):c.1166C>T(p.Ser389Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00719 in 1,613,790 control chromosomes in the GnomAD database, including 93 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0070 ( 16 hom., cov: 33)
Exomes 𝑓: 0.0072 ( 77 hom. )
Consequence
SLCO1C1
ENST00000266509.7 missense
ENST00000266509.7 missense
Scores
7
6
5
Clinical Significance
Conservation
PhyloP100: 7.32
Genes affected
SLCO1C1 (HGNC:13819): (solute carrier organic anion transporter family member 1C1) This gene encodes a member of the organic anion transporter family. The encoded protein is a transmembrane receptor that mediates the sodium-independent uptake of thyroid hormones in brain tissues. This protein has particularly high affinity for the thyroid hormones thyroxine, tri-iodothyronine and reverse tri-iodothyronine. Polymorphisms in the gene encoding this protein may be associated with fatigue and depression in patients suffering from hyperthyroidism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.008827329).
BP6
Variant 12-20723234-C-T is Benign according to our data. Variant chr12-20723234-C-T is described in ClinVar as [Benign]. Clinvar id is 790367.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-20723234-C-T is described in Lovd as [Likely_benign].
BS2
High Homozygotes in GnomAd4 at 16 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLCO1C1 | NM_017435.5 | c.1166C>T | p.Ser389Phe | missense_variant | 9/15 | ENST00000266509.7 | NP_059131.1 | |
SLCO1C1 | NM_001145946.2 | c.1166C>T | p.Ser389Phe | missense_variant | 10/16 | NP_001139418.1 | ||
SLCO1C1 | NM_001145945.2 | c.1019C>T | p.Ser340Phe | missense_variant | 9/15 | NP_001139417.1 | ||
SLCO1C1 | NM_001145944.2 | c.812C>T | p.Ser271Phe | missense_variant | 7/13 | NP_001139416.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLCO1C1 | ENST00000266509.7 | c.1166C>T | p.Ser389Phe | missense_variant | 9/15 | 1 | NM_017435.5 | ENSP00000266509 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00699 AC: 1063AN: 152156Hom.: 16 Cov.: 33
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GnomAD3 exomes AF: 0.00749 AC: 1881AN: 250988Hom.: 20 AF XY: 0.00765 AC XY: 1038AN XY: 135670
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GnomAD4 exome AF: 0.00721 AC: 10534AN: 1461516Hom.: 77 Cov.: 31 AF XY: 0.00721 AC XY: 5241AN XY: 727054
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GnomAD4 genome AF: 0.00698 AC: 1063AN: 152274Hom.: 16 Cov.: 33 AF XY: 0.00831 AC XY: 619AN XY: 74446
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;T;.;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D
MetaRNN
Benign
T;T;T;T
MetaSVM
Uncertain
T
MutationAssessor
Pathogenic
.;M;M;.
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D;D
REVEL
Uncertain
Sift
Pathogenic
D;D;D;D
Sift4G
Pathogenic
D;D;D;D
Polyphen
1.0
.;D;.;.
Vest4
MVP
ClinPred
T
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at