rs746853821
Variant names:
Your query was ambiguous. Multiple possible variants found:
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-T
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
- chrX-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP3BS2_Supporting
The NM_000044.6(AR):c.1379_1420delGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG(p.Gly460_Gly473del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000769 in 559,316 control chromosomes in the GnomAD database, including 7 homozygotes. There are 14 hemizygotes in GnomAD. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G460G) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.000048 ( 0 hom., 3 hem., cov: 0)
Exomes 𝑓: 0.000082 ( 7 hom. 11 hem. )
Consequence
AR
NM_000044.6 disruptive_inframe_deletion
NM_000044.6 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.29
Publications
6 publications found
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]
AR Gene-Disease associations (from GenCC):
- androgen insensitivity syndromeInheritance: XL Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Laboratory for Molecular Medicine, G2P, Labcorp Genetics (formerly Invitae)
- Kennedy diseaseInheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, ClinGen, G2P, Labcorp Genetics (formerly Invitae), Orphanet
- partial androgen insensitivity syndromeInheritance: XL Classification: STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Orphanet
- complete androgen insensitivity syndromeInheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_000044.6
BS2
High Hemizygotes in GnomAd4 at 3 XL geneVariant has number of hemizygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_000044.6. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| AR | MANE Select | c.1379_1420delGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG | p.Gly460_Gly473del | disruptive_inframe_deletion | Exon 1 of 8 | NP_000035.2 | |||
| AR | c.1379_1420delGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG | p.Gly460_Gly473del | disruptive_inframe_deletion | Exon 1 of 4 | NP_001334992.1 | Q9NUA2 | |||
| AR | c.1379_1420delGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG | p.Gly460_Gly473del | disruptive_inframe_deletion | Exon 1 of 4 | NP_001334990.1 | Q9NUA2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| AR | TSL:1 MANE Select | c.1379_1420delGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG | p.Gly460_Gly473del | disruptive_inframe_deletion | Exon 1 of 8 | ENSP00000363822.3 | P10275-1 | ||
| AR | TSL:1 | c.1379_1420delGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG | p.Gly460_Gly473del | disruptive_inframe_deletion | Exon 1 of 5 | ENSP00000379359.3 | F5GZG9 | ||
| AR | TSL:1 | c.1379_1420delGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCG | p.Gly460_Gly473del | disruptive_inframe_deletion | Exon 1 of 4 | ENSP00000421155.1 | P10275-3 |
Frequencies
GnomAD3 genomes 0.0000482 AC: 4AN: 83058Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
4
AN:
83058
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0000819 AC: 39AN: 476258Hom.: 7 AF XY: 0.0000930 AC XY: 11AN XY: 118246 show subpopulations
GnomAD4 exome
AF:
AC:
39
AN:
476258
Hom.:
AF XY:
AC XY:
11
AN XY:
118246
show subpopulations
African (AFR)
AF:
AC:
1
AN:
13219
American (AMR)
AF:
AC:
5
AN:
8585
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
9546
East Asian (EAS)
AF:
AC:
1
AN:
14099
South Asian (SAS)
AF:
AC:
12
AN:
14720
European-Finnish (FIN)
AF:
AC:
0
AN:
21867
Middle Eastern (MID)
AF:
AC:
0
AN:
1305
European-Non Finnish (NFE)
AF:
AC:
19
AN:
372313
Other (OTH)
AF:
AC:
1
AN:
20604
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.718
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
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4
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<30
30-35
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Age
GnomAD4 genome 0.0000482 AC: 4AN: 83058Hom.: 0 Cov.: 0 AF XY: 0.000180 AC XY: 3AN XY: 16622 show subpopulations
GnomAD4 genome
AF:
AC:
4
AN:
83058
Hom.:
Cov.:
0
AF XY:
AC XY:
3
AN XY:
16622
show subpopulations
African (AFR)
AF:
AC:
1
AN:
21639
American (AMR)
AF:
AC:
3
AN:
7805
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2222
East Asian (EAS)
AF:
AC:
0
AN:
2575
South Asian (SAS)
AF:
AC:
0
AN:
1527
European-Finnish (FIN)
AF:
AC:
0
AN:
2382
Middle Eastern (MID)
AF:
AC:
0
AN:
195
European-Non Finnish (NFE)
AF:
AC:
0
AN:
43140
Other (OTH)
AF:
AC:
0
AN:
1060
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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