Genetic Variant RBMX:n.*3215_*3217delTAT (chrX-136872324-CATA-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PM4_SupportingBP6BS2

The NM_001164803.2(RBMX):c.559_561delTAT(p.Tyr187del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00545 in 1,164,703 control chromosomes in the GnomAD database, including 15 homozygotes. There are 2,098 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.0041 ( 2 hom., 131 hem., cov: 22)

Exomes 𝑓: 0.0056 ( 13 hom. 1967 hem. )

Consequence

RBMX
NM_001164803.2 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.35

Variant links:

Genes affected

RBMX (HGNC:9910): (RNA binding motif protein X-linked) This gene belongs to the RBMY gene family which includes candidate Y chromosome spermatogenesis genes. This gene, an active X chromosome homolog of the Y chromosome RBMY gene, is widely expressed whereas the RBMY gene evolved a male-specific function in spermatogenesis. Pseudogenes of this gene, found on chromosomes 1, 4, 9, 11, and 6, were likely derived by retrotransposition from the original gene. Alternatively spliced transcript variants encoding different isoforms have been identified. A snoRNA gene (SNORD61) is found in one of its introns. [provided by RefSeq, Sep 2009]

RBMX links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_001164803.2. Strenght limited to Supporting due to length of the change: 1aa.

BP6

Variant X-136872324-CATA-C is Benign according to our data. Variant chrX-136872324-CATA-C is described in ClinVar as [Benign]. Clinvar id is 3033241.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Homozygotes in GnomAd4 at 2 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBMX	NM_001164803.2 link	c.559_561delTAT	p.Tyr187del	conservative_inframe_deletion	Exon 7 of 8		NP_001158275.1	P38159-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	Protein	UniProt
RBMX	ENST00000568578.5 link	n.3215_3217delTAT		non_coding_transcript_exon_variant	Exon 7 of 8	1	ENSP00000457691.1	H3BR27
RBMX	ENST00000568578.5 link	n.3215_3217delTAT		3_prime_UTR_variant	Exon 7 of 8	1	ENSP00000457691.1	H3BR27
RBMX	ENST00000431446.7 link	c.559_561delTAT	p.Tyr187del	conservative_inframe_deletion	Exon 7 of 8	2	ENSP00000411989.3	P38159-3

Frequencies

GnomAD3 genomes

AF:

0.00414

AC:

465

AN:

112190

Hom.:

Cov.:

AF XY:

0.00384

AC XY:

132

AN XY:

34352

show subpopulations

Gnomad AFR

AF:

0.000906

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00152

Gnomad ASJ

AF:

0.00718

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00294

Gnomad FIN

AF:

0.00295

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00695

Gnomad OTH

AF:

0.00400

GnomAD3 exomes

AF:

0.00461

AC:

534

AN:

115914

Hom.:

AF XY:

0.00491

AC XY:

202

AN XY:

41132

show subpopulations

Gnomad AFR exome

AF:

0.000755

Gnomad AMR exome

AF:

0.000672

Gnomad ASJ exome

AF:

0.00910

Gnomad EAS exome

AF:

0.000123

Gnomad SAS exome

AF:

0.00495

Gnomad FIN exome

AF:

0.00310

Gnomad NFE exome

AF:

0.00730

Gnomad OTH exome

AF:

0.00543

GnomAD4 exome

AF:

0.00559

AC:

5881

AN:

1052464

Hom.:

AF XY:

0.00573

AC XY:

1967

AN XY:

343118

show subpopulations

Gnomad4 AFR exome

AF:

0.000965

Gnomad4 AMR exome

AF:

0.000789

Gnomad4 ASJ exome

AF:

0.00961

Gnomad4 EAS exome

AF:

0.0000369

Gnomad4 SAS exome

AF:

0.00649

Gnomad4 FIN exome

AF:

0.00429

Gnomad4 NFE exome

AF:

0.00605

Gnomad4 OTH exome

AF:

0.00459

GnomAD4 genome

AF:

0.00413

AC:

464

AN:

112239

Hom.:

Cov.:

AF XY:

0.00381

AC XY:

131

AN XY:

34413

show subpopulations

Gnomad4 AFR

AF:

0.000904

Gnomad4 AMR

AF:

0.00152

Gnomad4 ASJ

AF:

0.00718

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00295

Gnomad4 FIN

AF:

0.00295

Gnomad4 NFE

AF:

0.00693

Gnomad4 OTH

AF:

0.00395

Alfa

AF:

0.00567

Hom.:

Bravo

AF:

0.00386

Asia WGS

AF:

0.00438

AC:

AN:

2522

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

RBMX-related disorder

Benign:1

Dec 06, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

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