chrX-67546514-TGGCGGCGGCGGCGGCGGCGGC-T
Variant summary
Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_000044.6(AR):c.1400_1420delGCGGCGGCGGCGGCGGCGGCG(p.Gly467_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 0.0128 in 558,215 control chromosomes in the GnomAD database, including 548 homozygotes. There are 2,000 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. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. G467G) has been classified as Likely benign.
Frequency
Consequence
NM_000044.6 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
Publications
- androgen insensitivity syndromeInheritance: XL Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine
- Kennedy diseaseInheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, ClinGen, G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- partial androgen insensitivity syndromeInheritance: XL Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Genomics England PanelApp
- complete androgen insensitivity syndromeInheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AR | NM_000044.6 | c.1400_1420delGCGGCGGCGGCGGCGGCGGCG | p.Gly467_Gly473del | disruptive_inframe_deletion | Exon 1 of 8 | ENST00000374690.9 | NP_000035.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00609 AC: 506AN: 83052Hom.: 2 Cov.: 0 show subpopulations
GnomAD2 exomes AF: 0.0121 AC: 455AN: 37570 AF XY: 0.00840 show subpopulations
GnomAD4 exome AF: 0.0140 AC: 6641AN: 475159Hom.: 545 AF XY: 0.0160 AC XY: 1882AN XY: 117809 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00615 AC: 511AN: 83056Hom.: 3 Cov.: 0 AF XY: 0.00710 AC XY: 118AN XY: 16626 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Benign:1
- -
Androgen resistance syndrome;C1839259:Kennedy disease Benign:1
- -
not provided Benign:1
AR: BS1, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at