Variant X-67546514-TGGCGGCGGCGGCGGCGGC-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2

The NM_000044.6(AR):c.1403_1420del(p.Gly468_Gly473del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0251 in 558,345 control chromosomes in the GnomAD database, including 1,198 homozygotes. There are 3,999 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. G457G) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.011 ( 7 hom., 172 hem., cov: 0)

Exomes 𝑓: 0.028 ( 1191 hom. 3827 hem. )

Consequence

AR
NM_000044.6 inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

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-TGGCGGCGGCGGCGGCGGC-T is Benign according to our data. Variant chrX-67546514-TGGCGGCGGCGGCGGCGGC-T is described in ClinVar as [Benign]. Clinvar id is 1168910.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-67546514-TGGCGGCGGCGGCGGCGGC-T is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.0276 (13127/475300) while in subpopulation SAS AF= 0.0455 (667/14650). AF 95% confidence interval is 0.0427. There are 1191 homozygotes in gnomad4_exome. There are 3827 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 7 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AR	NM_000044.6 linkuse as main transcript	c.1403_1420del	p.Gly468_Gly473del	inframe_deletion	1/8	ENST00000374690.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AR	ENST00000374690.9 linkuse as main transcript	c.1403_1420del	p.Gly468_Gly473del	inframe_deletion	1/8	1	NM_000044.6	P1	P10275-1

Frequencies

GnomAD3 genomes

AF:

0.0110

AC:

912

AN:

83041

Hom.:

Cov.:

AF XY:

0.0104

AC XY:

172

AN XY:

16605

show subpopulations

Gnomad AFR

AF:

0.00499

Gnomad AMI

AF:

0.136

Gnomad AMR

AF:

0.00666

Gnomad ASJ

AF:

0.00945

Gnomad EAS

AF:

0.00272

Gnomad SAS

AF:

0.0131

Gnomad FIN

AF:

0.00672

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0142

Gnomad OTH

AF:

0.00660

GnomAD3 exomes

AF:

0.0287

AC:

1079

AN:

37570

Hom.:

294

AF XY:

0.0225

AC XY:

292

AN XY:

12980

show subpopulations

Gnomad AFR exome

AF:

0.0272

Gnomad AMR exome

AF:

0.0447

Gnomad ASJ exome

AF:

0.0211

Gnomad EAS exome

AF:

0.0256

Gnomad SAS exome

AF:

0.0297

Gnomad FIN exome

AF:

0.00673

Gnomad NFE exome

AF:

0.0376

Gnomad OTH exome

AF:

0.0284

GnomAD4 exome

AF:

0.0276

AC:

13127

AN:

475300

Hom.:

1191

AF XY:

0.0325

AC XY:

3827

AN XY:

117708

show subpopulations

Gnomad4 AFR exome

AF:

0.00793

Gnomad4 AMR exome

AF:

0.0270

Gnomad4 ASJ exome

AF:

0.0238

Gnomad4 EAS exome

AF:

0.00633

Gnomad4 SAS exome

AF:

0.0455

Gnomad4 FIN exome

AF:

0.0121

Gnomad4 NFE exome

AF:

0.0297

Gnomad4 OTH exome

AF:

0.0231

GnomAD4 genome

AF:

0.0110

AC:

912

AN:

83045

Hom.:

Cov.:

AF XY:

0.0104

AC XY:

172

AN XY:

16615

show subpopulations

Gnomad4 AFR

AF:

0.00499

Gnomad4 AMR

AF:

0.00665

Gnomad4 ASJ

AF:

0.00945

Gnomad4 EAS

AF:

0.00273

Gnomad4 SAS

AF:

0.0131

Gnomad4 FIN

AF:

0.00672

Gnomad4 NFE

AF:

0.0142

Gnomad4 OTH

AF:

0.00651

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Androgen resistance syndrome;C1839259:Kennedy disease

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

May 01, 2024

AR: BS1, BS2 -

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