Variant X-67545316-TGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA-TGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_000044.6(AR):c.231_239dup(p.Gln78_Gln80dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0236 in 988,999 control chromosomes in the GnomAD database, including 363 homozygotes. There are 1,465 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.063 ( 211 hom., 319 hem., cov: 0)

Exomes 𝑓: 0.021 ( 152 hom. 1146 hem. )

Consequence

AR
NM_000044.6 inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:4

Conservation

PhyloP100: 0.337

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 -10 ACMG points.

BP6

Variant X-67545316-T-TGCAGCAGCA is Benign according to our data. Variant chrX-67545316-T-TGCAGCAGCA is described in ClinVar as [Benign]. Clinvar id is 464797.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AR	NM_000044.6 linkuse as main transcript	c.231_239dup	p.Gln78_Gln80dup	inframe_insertion	1/8	ENST00000374690.9	NP_000035.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AR	ENST00000374690.9 linkuse as main transcript	c.231_239dup	p.Gln78_Gln80dup	inframe_insertion	1/8	1	NM_000044.6	ENSP00000363822	P1	P10275-1

Frequencies

GnomAD3 genomes

AF:

0.0635

AC:

4232

AN:

66600

Hom.:

213

Cov.:

AF XY:

0.0387

AC XY:

319

AN XY:

8240

show subpopulations

Gnomad AFR

AF:

0.0334

Gnomad AMI

AF:

0.0381

Gnomad AMR

AF:

0.0840

Gnomad ASJ

AF:

0.124

Gnomad EAS

AF:

0.0891

Gnomad SAS

AF:

0.0692

Gnomad FIN

AF:

0.0856

Gnomad MID

AF:

0.0654

Gnomad NFE

AF:

0.0708

Gnomad OTH

AF:

0.0848

GnomAD4 exome

AF:

0.0207

AC:

19133

AN:

922412

Hom.:

152

Cov.:

AF XY:

0.00408

AC XY:

1146

AN XY:

281002

show subpopulations

Gnomad4 AFR exome

AF:

0.0117

Gnomad4 AMR exome

AF:

0.0402

Gnomad4 ASJ exome

AF:

0.0488

Gnomad4 EAS exome

AF:

0.0490

Gnomad4 SAS exome

AF:

0.0225

Gnomad4 FIN exome

AF:

0.0748

Gnomad4 NFE exome

AF:

0.0153

Gnomad4 OTH exome

AF:

0.0302

GnomAD4 genome

AF:

0.0635

AC:

4227

AN:

66587

Hom.:

211

Cov.:

AF XY:

0.0387

AC XY:

319

AN XY:

8253

show subpopulations

Gnomad4 AFR

AF:

0.0335

Gnomad4 AMR

AF:

0.0837

Gnomad4 ASJ

AF:

0.124

Gnomad4 EAS

AF:

0.0879

Gnomad4 SAS

AF:

0.0667

Gnomad4 FIN

AF:

0.0856

Gnomad4 NFE

AF:

0.0709

Gnomad4 OTH

AF:

0.0887

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:3

Likely benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 03, 2015	- -
Likely benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -

not specified

Benign:1

Benign, no assertion criteria provided

clinical testing

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

- -

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.

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