X-67545316-TGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA-TGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_000044.6(AR):c.225_239dupGCAGCAGCAGCAGCA(p.Gln76_Gln80dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.020 ( 36 hom., 74 hem., cov: 0)
Exomes 𝑓: 0.0067 ( 10 hom. 419 hem. )
Failed GnomAD Quality Control
Consequence
AR
NM_000044.6 disruptive_inframe_insertion
NM_000044.6 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.337
Genes affected
AR (HGNC:644): (androgen receptor) The androgen receptor gene is more than 90 kb long and codes for a protein that has 3 major functional domains: the N-terminal domain, DNA-binding domain, and androgen-binding domain. The protein functions as a steroid-hormone activated transcription factor. Upon binding the hormone ligand, the receptor dissociates from accessory proteins, translocates into the nucleus, dimerizes, and then stimulates transcription of androgen responsive genes. This gene contains 2 polymorphic trinucleotide repeat segments that encode polyglutamine and polyglycine tracts in the N-terminal transactivation domain of its protein. Expansion of the polyglutamine tract from the normal 9-34 repeats to the pathogenic 38-62 repeats causes spinal bulbar muscular atrophy (SBMA, also known as Kennedy's disease). Mutations in this gene are also associated with complete androgen insensitivity (CAIS). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
Variant X-67545316-T-TGCAGCAGCAGCAGCA is Benign according to our data. Variant chrX-67545316-T-TGCAGCAGCAGCAGCA is described in ClinVar as [Benign]. Clinvar id is 464795.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0196 (1304/66608) while in subpopulation EAS AF= 0.0402 (74/1841). AF 95% confidence interval is 0.0328. There are 36 homozygotes in gnomad4. There are 74 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 36 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AR | NM_000044.6 | c.225_239dupGCAGCAGCAGCAGCA | p.Gln76_Gln80dup | disruptive_inframe_insertion | 1/8 | ENST00000374690.9 | NP_000035.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0196 AC: 1304AN: 66621Hom.: 36 Cov.: 0 AF XY: 0.00898 AC XY: 74AN XY: 8243
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00673 AC: 6273AN: 932512Hom.: 10 Cov.: 40 AF XY: 0.00144 AC XY: 419AN XY: 290870
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GnomAD4 genome AF: 0.0196 AC: 1304AN: 66608Hom.: 36 Cov.: 0 AF XY: 0.00896 AC XY: 74AN XY: 8256
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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
Likely benign, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | The AR p.Gln76_Gln80dup variant was not identified in the literature nor was it identified in the dbSNP, COGR, Cosmic, MutDB, and UMD-LSDB databases. The variant was also identified in ClinVar as benign with one submission from Invitae with the associated conditions of Androgen resistance syndrome and Bulbo-spinal atrophy X-linked. The variant was also identified in LOVD 3.0. The variant was not identified in the following control databases: the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). This variant is an in-frame insertion resulting in the duplication of a glutamine (gln) residue at codon 76; the impact of this alteration on AR protein function is not known, however this insertion occurs in a variable poly-Q repeat region and was predicted to be a polymorphism by MutationTaster. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign. - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 06, 2016 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jul 25, 2023 | Variant summary: AR c.225_239dup15 (p.Gln76_Gln80dup) results in an in-frame duplication that is predicted to duplicate five amino acids into the encoded protein. Diagnosis of Spinal and bulbar muscular atrophy is established based on the identification of an expansion of CAG trinucleotide repeat of >35 CAGs whereas the current variant involves 28 CAGs. Additionally, this in-frame duplication is not consistent with the molecular mechanism of disease for Androgen Resistance Syndrome. The variant was absent in 166414 control chromosomes, however this region of the gene in gnomad contains numerous high frequency duplications/deletions, with dubious quality annotation due to low complexity region. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.225_239dup15 has been reported in the literature in an individual affected with Hypospadias (Xie_2012). These data do not allow any conclusion about variant significance. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication have been ascertained in the context of this evaluation (PMID: 35729303). Two submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as benign. Based on the evidence outlined above, the variant was classified as benign. - |
Androgen resistance syndrome;C1839259:Kennedy disease Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at