chr12-20740175-G-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_017435.5(SLCO1C1):c.1549-9G>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00293 in 1,598,082 control chromosomes in the GnomAD database, including 98 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.014 ( 55 hom., cov: 31)
Exomes 𝑓: 0.0017 ( 43 hom. )
Consequence
SLCO1C1
NM_017435.5 splice_polypyrimidine_tract, intron
NM_017435.5 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.00001958
2
Clinical Significance
Conservation
PhyloP100: 0.0230
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 12-20740175-G-T is Benign according to our data. Variant chr12-20740175-G-T is described in ClinVar as [Benign]. Clinvar id is 710132.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-20740175-G-T is described in Lovd as [Benign].
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0143 (2179/152070) while in subpopulation AFR AF= 0.0475 (1971/41468). AF 95% confidence interval is 0.0458. There are 55 homozygotes in gnomad4. There are 982 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 55 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLCO1C1 | NM_017435.5 | c.1549-9G>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000266509.7 | |||
SLCO1C1 | NM_001145944.2 | c.1195-9G>T | splice_polypyrimidine_tract_variant, intron_variant | ||||
SLCO1C1 | NM_001145945.2 | c.1402-9G>T | splice_polypyrimidine_tract_variant, intron_variant | ||||
SLCO1C1 | NM_001145946.2 | c.1549-9G>T | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLCO1C1 | ENST00000266509.7 | c.1549-9G>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_017435.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0143 AC: 2180AN: 151952Hom.: 55 Cov.: 31
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GnomAD3 exomes AF: 0.00407 AC: 967AN: 237472Hom.: 26 AF XY: 0.00299 AC XY: 385AN XY: 128668
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GnomAD4 exome AF: 0.00173 AC: 2502AN: 1446012Hom.: 43 Cov.: 33 AF XY: 0.00156 AC XY: 1119AN XY: 719150
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GnomAD4 genome AF: 0.0143 AC: 2179AN: 152070Hom.: 55 Cov.: 31 AF XY: 0.0132 AC XY: 982AN XY: 74328
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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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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at