chr12-20733007-T-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_017435.5(SLCO1C1):c.1285T>C(p.Leu429=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00101 in 1,613,880 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0061 ( 11 hom., cov: 32)
Exomes 𝑓: 0.00048 ( 3 hom. )
Consequence
SLCO1C1
NM_017435.5 synonymous
NM_017435.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.364
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
?
Variant 12-20733007-T-C is Benign according to our data. Variant chr12-20733007-T-C is described in ClinVar as [Benign]. Clinvar id is 716429.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.364 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00609 (927/152268) while in subpopulation AFR AF= 0.0216 (898/41544). AF 95% confidence interval is 0.0204. There are 11 homozygotes in gnomad4. There are 454 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLCO1C1 | NM_017435.5 | c.1285T>C | p.Leu429= | synonymous_variant | 10/15 | ENST00000266509.7 | |
SLCO1C1 | NM_001145946.2 | c.1285T>C | p.Leu429= | synonymous_variant | 11/16 | ||
SLCO1C1 | NM_001145945.2 | c.1138T>C | p.Leu380= | synonymous_variant | 10/15 | ||
SLCO1C1 | NM_001145944.2 | c.931T>C | p.Leu311= | synonymous_variant | 8/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO1C1 | ENST00000266509.7 | c.1285T>C | p.Leu429= | synonymous_variant | 10/15 | 1 | NM_017435.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00598 AC: 910AN: 152150Hom.: 8 Cov.: 32
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GnomAD3 exomes AF: 0.00155 AC: 388AN: 251036Hom.: 2 AF XY: 0.00113 AC XY: 153AN XY: 135690
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GnomAD4 exome AF: 0.000484 AC: 708AN: 1461612Hom.: 3 Cov.: 31 AF XY: 0.000418 AC XY: 304AN XY: 727086
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GnomAD4 genome ? AF: 0.00609 AC: 927AN: 152268Hom.: 11 Cov.: 32 AF XY: 0.00610 AC XY: 454AN XY: 74462
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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 | Invitae | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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