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

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.337
Variant links:
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
ARNM_000044.6 linkc.225_239dupGCAGCAGCAGCAGCA p.Gln76_Gln80dup disruptive_inframe_insertion 1/8 ENST00000374690.9 NP_000035.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ARENST00000374690.9 linkc.225_239dupGCAGCAGCAGCAGCA p.Gln76_Gln80dup disruptive_inframe_insertion 1/81 NM_000044.6 ENSP00000363822.3 P10275-1

Frequencies

GnomAD3 genomes
AF:
0.0196
AC:
1304
AN:
66621
Hom.:
36
Cov.:
0
AF XY:
0.00898
AC XY:
74
AN XY:
8243
show subpopulations
Gnomad AFR
AF:
0.0118
Gnomad AMI
AF:
0.0112
Gnomad AMR
AF:
0.0251
Gnomad ASJ
AF:
0.0274
Gnomad EAS
AF:
0.0400
Gnomad SAS
AF:
0.0263
Gnomad FIN
AF:
0.0222
Gnomad MID
AF:
0.0327
Gnomad NFE
AF:
0.0213
Gnomad OTH
AF:
0.0150
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00673
AC:
6273
AN:
932512
Hom.:
10
Cov.:
40
AF XY:
0.00144
AC XY:
419
AN XY:
290870
show subpopulations
Gnomad4 AFR exome
AF:
0.00380
Gnomad4 AMR exome
AF:
0.0141
Gnomad4 ASJ exome
AF:
0.0132
Gnomad4 EAS exome
AF:
0.0262
Gnomad4 SAS exome
AF:
0.00757
Gnomad4 FIN exome
AF:
0.0180
Gnomad4 NFE exome
AF:
0.00491
Gnomad4 OTH exome
AF:
0.00895
GnomAD4 genome
AF:
0.0196
AC:
1304
AN:
66608
Hom.:
36
Cov.:
0
AF XY:
0.00896
AC XY:
74
AN XY:
8256
show subpopulations
Gnomad4 AFR
AF:
0.0118
Gnomad4 AMR
AF:
0.0250
Gnomad4 ASJ
AF:
0.0274
Gnomad4 EAS
AF:
0.0402
Gnomad4 SAS
AF:
0.0266
Gnomad4 FIN
AF:
0.0222
Gnomad4 NFE
AF:
0.0213
Gnomad4 OTH
AF:
0.0148

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 providedclinical testingDepartment 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 submitterclinical testingGeneDxJul 06, 2016- -
not specified Benign:1
Benign, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpJul 25, 2023Variant 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 submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 31, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3032358; hg19: chrX-66765158; API