chrX-74421518-G-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_006517.5(SLC16A2):c.-120G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 968,048 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 22 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000054 ( 0 hom., 1 hem., cov: 22)
Exomes 𝑓: 0.00012 ( 0 hom. 21 hem. )
Consequence
SLC16A2
NM_006517.5 5_prime_UTR
NM_006517.5 5_prime_UTR
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 0.834
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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
Variant X-74421518-G-A is Benign according to our data. Variant chrX-74421518-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 675273.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.000116 (99/856742) while in subpopulation NFE AF= 0.000147 (94/638641). AF 95% confidence interval is 0.000123. There are 0 homozygotes in gnomad4_exome. There are 21 alleles in male gnomad4_exome subpopulation. Median coverage is 15. This position pass quality control queck.
BS2
High Hemizygotes in GnomAdExome4 at 21 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC16A2 | NM_006517.5 | c.-120G>A | 5_prime_UTR_variant | 1/6 | ENST00000587091.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC16A2 | ENST00000587091.6 | c.-120G>A | 5_prime_UTR_variant | 1/6 | 1 | NM_006517.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000539 AC: 6AN: 111306Hom.: 0 Cov.: 22 AF XY: 0.0000298 AC XY: 1AN XY: 33534
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GnomAD3 exomes AF: 0.0000339 AC: 4AN: 118094Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 38038
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GnomAD4 exome AF: 0.000116 AC: 99AN: 856742Hom.: 0 Cov.: 15 AF XY: 0.0000874 AC XY: 21AN XY: 240266
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GnomAD4 genome AF: 0.0000539 AC: 6AN: 111306Hom.: 0 Cov.: 22 AF XY: 0.0000298 AC XY: 1AN XY: 33534
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 09, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at