chrX-67546514-T-TGGCGGCGGCGGCGGC

Variant names:

• chrX-67546514-T-TGGCGGCGGCGGCGGC
• rs746853821
• NM_000044.6:c.1406_1420dupGCGGCGGCGGCGGCG

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP3 BS2

The NM_000044.6(AR):​c.1406_1420dupGCGGCGGCGGCGGCG​(p.Gly469_Gly473dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_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. E474E) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.0013 (1 hom., 9 hem., cov: 0)
  • Exomes 𝑓: 0.00021 (0 hom. 33 hem.)
  • Failed GnomAD Quality Control
• Consequence: AR NM_000044.6 disruptive_inframe_insertion
• 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 syndrome

  Inheritance: XL Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Laboratory for Molecular Medicine, G2P, Labcorp Genetics (formerly Invitae)
• Kennedy disease

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, ClinGen, G2P, Labcorp Genetics (formerly Invitae), Orphanet
• partial androgen insensitivity syndrome

  Inheritance: XL Classification: STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Orphanet
• complete androgen insensitivity syndrome

  Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_000044.6
• BS2: High Hemizygotes in GnomAd4 at 9 XL gene

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	NM_000044.6	MANE Select	c.1406_1420dupGCGGCGGCGGCGGCG	p.Gly469_Gly473dup	disruptive_inframe_insertion	Exon 1 of 8	NP_000035.2
	AR	NM_001348063.1		c.1406_1420dupGCGGCGGCGGCGGCG	p.Gly469_Gly473dup	disruptive_inframe_insertion	Exon 1 of 4	NP_001334992.1	Q9NUA2
	AR	NM_001348061.1		c.1406_1420dupGCGGCGGCGGCGGCG	p.Gly469_Gly473dup	disruptive_inframe_insertion	Exon 1 of 4	NP_001334990.1	Q9NUA2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AR	ENST00000374690.9	TSL:1 MANE Select	c.1406_1420dupGCGGCGGCGGCGGCG	p.Gly469_Gly473dup	disruptive_inframe_insertion	Exon 1 of 8	ENSP00000363822.3	P10275-1
	AR	ENST00000396044.8	TSL:1	c.1406_1420dupGCGGCGGCGGCGGCG	p.Gly469_Gly473dup	disruptive_inframe_insertion	Exon 1 of 5	ENSP00000379359.3	F5GZG9
	AR	ENST00000504326.5	TSL:1	c.1406_1420dupGCGGCGGCGGCGGCG	p.Gly469_Gly473dup	disruptive_inframe_insertion	Exon 1 of 4	ENSP00000421155.1	P10275-3

Frequencies

GnomAD3 genomes AF: 0.00126 AC: 105 AN: 83058 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.00379

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000897

Gnomad ASJ AF: 0.000450

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000655

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000325

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000206 AC: 98 AN: 476289 Hom.: 0 Cov.: 25 AF XY: 0.000279 AC XY: 33 AN XY: 118279

African (AFR) AF: 0.000908 AC: 12 AN: 13218

American (AMR) AF: 0.00 AC: 0 AN: 8585

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9550

East Asian (EAS) AF: 0.00 AC: 0 AN: 14101

South Asian (SAS) AF: 0.000204 AC: 3 AN: 14721

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21872

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1306

European-Non Finnish (NFE) AF: 0.000201 AC: 75 AN: 372332

Other (OTH) AF: 0.000388 AC: 8 AN: 20604

GnomAD4 genome AF: 0.00126 AC: 105 AN: 83062 Hom.: 1 Cov.: 0 AF XY: 0.000541 AC XY: 9 AN XY: 16632

African (AFR) AF: 0.00379 AC: 82 AN: 21655

American (AMR) AF: 0.000895 AC: 7 AN: 7817

Ashkenazi Jewish (ASJ) AF: 0.000450 AC: 1 AN: 2222

East Asian (EAS) AF: 0.00 AC: 0 AN: 2564

South Asian (SAS) AF: 0.000657 AC: 1 AN: 1522

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2382

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 174

European-Non Finnish (NFE) AF: 0.000325 AC: 14 AN: 43137

Other (OTH) AF: 0.00 AC: 0 AN: 1076

Alfa AF: 0.00 Hom.: 327

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs746853821; hg19: chrX-66766356;