chrX-67545313-TGCTGCAGCAGCAGCA-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM4BP6_ModerateBS2
The NM_000044.6(AR):c.170_184del(p.Leu57_Gln61del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000182 in 1,099,097 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00013 ( 0 hom., 4 hem., cov: 0)
Exomes 𝑓: 0.0000098 ( 0 hom. 0 hem. )
Consequence
AR
NM_000044.6 inframe_deletion
NM_000044.6 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.40
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 Likely_benign. Variant got -4 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_000044.6.
BP6
?
Variant X-67545313-TGCTGCAGCAGCAGCA-T is Benign according to our data. Variant chrX-67545313-TGCTGCAGCAGCAGCA-T is described in ClinVar as [Benign]. Clinvar id is 3043532.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Hemizygotes in GnomAd at 4 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AR | NM_000044.6 | c.170_184del | p.Leu57_Gln61del | inframe_deletion | 1/8 | ENST00000374690.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AR | ENST00000374690.9 | c.170_184del | p.Leu57_Gln61del | inframe_deletion | 1/8 | 1 | NM_000044.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000134 AC: 10AN: 74555Hom.: 0 Cov.: 0 AF XY: 0.000273 AC XY: 4AN XY: 14661
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GnomAD4 exome AF: 0.00000976 AC: 10AN: 1024541Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 326635
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GnomAD4 genome ? AF: 0.000134 AC: 10AN: 74556Hom.: 0 Cov.: 0 AF XY: 0.000273 AC XY: 4AN XY: 14676
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
AR-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 01, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at