Genetic Variant AR:p.Gly471_Gly473del (chrX-67546514-TGGCGGCGGC-T) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_000044.6(AR):c.1412_1420delGCGGCGGCG(p.Gly471_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 0.0196 in 558,071 control chromosomes in the GnomAD database, including 733 homozygotes. There are 2,532 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.033 ( 77 hom., 461 hem., cov: 0)

Exomes 𝑓: 0.017 ( 656 hom. 2071 hem. )

Consequence

AR
NM_000044.6 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.29

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]

AR links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant X-67546514-TGGCGGCGGC-T is Benign according to our data. Variant chrX-67546514-TGGCGGCGGC-T is described in ClinVar as [Benign]. Clinvar id is 434264.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-67546514-TGGCGGCGGC-T is described in Lovd as [Likely_benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AR	NM_000044.6 link	c.1412_1420delGCGGCGGCG	p.Gly471_Gly473del	disruptive_inframe_deletion	Exon 1 of 8	ENST00000374690.9	NP_000035.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AR	ENST00000374690.9 link	c.1412_1420delGCGGCGGCG	p.Gly471_Gly473del	disruptive_inframe_deletion	Exon 1 of 8	1	NM_000044.6	ENSP00000363822.3		P10275-1

Frequencies

GnomAD3 genomes

AF:

0.0326

AC:

2708

AN:

83029

Hom.:

Cov.:

AF XY:

0.0278

AC XY:

461

AN XY:

16603

show subpopulations

Gnomad AFR

AF:

0.0927

Gnomad AMI

AF:

0.00195

Gnomad AMR

AF:

0.0140

Gnomad ASJ

AF:

0.0108

Gnomad EAS

AF:

0.0381

Gnomad SAS

AF:

0.0236

Gnomad FIN

AF:

0.00504

Gnomad MID

AF:

0.00513

Gnomad NFE

AF:

0.00927

Gnomad OTH

AF:

0.0217

GnomAD4 exome

AF:

0.0173

AC:

8211

AN:

475038

Hom.:

656

AF XY:

0.0176

AC XY:

2071

AN XY:

117396

show subpopulations

Gnomad4 AFR exome

AF:

0.104

Gnomad4 AMR exome

AF:

0.00970

Gnomad4 ASJ exome

AF:

0.00829

Gnomad4 EAS exome

AF:

0.0383

Gnomad4 SAS exome

AF:

0.0341

Gnomad4 FIN exome

AF:

0.00485

Gnomad4 NFE exome

AF:

0.0137

Gnomad4 OTH exome

AF:

0.0226

GnomAD4 genome

AF:

0.0326

AC:

2707

AN:

83033

Hom.:

Cov.:

AF XY:

0.0277

AC XY:

461

AN XY:

16613

show subpopulations

Gnomad4 AFR

AF:

0.0927

Gnomad4 AMR

AF:

0.0139

Gnomad4 ASJ

AF:

0.0108

Gnomad4 EAS

AF:

0.0374

Gnomad4 SAS

AF:

0.0224

Gnomad4 FIN

AF:

0.00504

Gnomad4 NFE

AF:

0.00927

Gnomad4 OTH

AF:

0.0233

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 10, 2021

Genetic Services Laboratory, University of Chicago

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Androgen resistance syndrome;C1839259:Kennedy disease

Benign:1

Dec 28, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Jun 21, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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.

X-67546514-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over