rs5937843
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000587091.6(SLC16A2):c.1399+43T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 110,541 control chromosomes in the GnomAD database, including 16,119 homozygotes. There are 18,552 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.58 ( 16119 hom., 18552 hem., cov: 22)
Exomes 𝑓: 0.75 ( 199128 hom. 204718 hem. )
Failed GnomAD Quality Control
Consequence
SLC16A2
ENST00000587091.6 intron
ENST00000587091.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0840
Genes affected
SLC16A2 (HGNC:10923): (solute carrier family 16 member 2) This gene encodes an integral membrane protein that functions as a transporter of thyroid hormone. The encoded protein facilitates the cellular importation of thyroxine (T4), triiodothyronine (T3), reverse triiodothyronine (rT3) and diidothyronine (T2). This gene is expressed in many tissues and likely plays an important role in the development of the central nervous system. Loss of function mutations in this gene are associated with psychomotor retardation in males while females exhibit no neurological defects and more moderate thyroid-deficient phenotypes. This gene is subject to X-chromosome inactivation. Mutations in this gene are the cause of Allan-Herndon-Dudley syndrome. [provided by RefSeq, Mar 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant X-74529484-T-G is Benign according to our data. Variant chrX-74529484-T-G is described in ClinVar as [Benign]. Clinvar id is 159903.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC16A2 | NM_006517.5 | c.1399+43T>G | intron_variant | ENST00000587091.6 | NP_006508.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC16A2 | ENST00000587091.6 | c.1399+43T>G | intron_variant | 1 | NM_006517.5 | ENSP00000465734 | P1 | |||
SLC16A2 | ENST00000590447.1 | c.611-1849T>G | intron_variant | 5 | ENSP00000466213 | |||||
SLC16A2 | ENST00000636771.1 | c.*1100+43T>G | intron_variant, NMD_transcript_variant | 5 | ENSP00000490445 |
Frequencies
GnomAD3 genomes AF: 0.576 AC: 63643AN: 110491Hom.: 16133 Cov.: 22 AF XY: 0.566 AC XY: 18520AN XY: 32747
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GnomAD3 exomes AF: 0.606 AC: 63477AN: 104815Hom.: 15361 AF XY: 0.616 AC XY: 20079AN XY: 32609
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GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.754 AC: 705707AN: 935708Hom.: 199128 Cov.: 16 AF XY: 0.760 AC XY: 204718AN XY: 269428
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Data not reliable, filtered out with message: InbreedingCoeff
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GnomAD4 genome AF: 0.576 AC: 63643AN: 110541Hom.: 16119 Cov.: 22 AF XY: 0.565 AC XY: 18552AN XY: 32807
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 2018 | - - |
not specified Benign:1
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | - - |
Allan-Herndon-Dudley syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
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