ENST00000562646.5:c.*606_*607insTGAGAGTTAC

Variant names:

• chrX-136874453-C-CGTAACTCTCA
• rs1256966146
• ENST00000562646.5:c.*606_*607insTGAGAGTTAC

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. PP3

The ENST00000562646.5(RBMX):​c.*606_*607insTGAGAGTTAC variant causes a 3 prime UTR change involving the alteration of a conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., 0 hem., cov: 22)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: RBMX ENST00000562646.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.89
• Publications: 1 publications found

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 Gene-Disease associations (from GenCC):

• syndromic X-linked intellectual disability Shashi type

  Inheritance: Unknown, XL Classification: MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562646.5. 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
	RBMX	NM_002139.4	MANE Select	c.866-2_866-1insTGAGAGTTAC		splice_acceptor intron	N/A	NP_002130.2	P38159-1
	RBMX	NM_001164803.2		c.540+632_540+633insTGAGAGTTAC		intron	N/A	NP_001158275.1	P38159-3
	RBMX	NR_028476.2		n.849-2_849-1insTGAGAGTTAC		splice_acceptor intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBMX	ENST00000562646.5	TSL:1	c.*606_*607insTGAGAGTTAC		3_prime_UTR	Exon 8 of 8	ENSP00000457051.1	H3BT71
	RBMX	ENST00000320676.11	TSL:1 MANE Select	c.866-2_866-1insTGAGAGTTAC		splice_acceptor intron	N/A	ENSP00000359645.3	P38159-1
	RBMX	ENST00000568578.5	TSL:1	n.*1088_*1089insTGAGAGTTAC		non_coding_transcript_exon	Exon 7 of 8	ENSP00000457691.1	H3BR27

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 112030 Hom.: 0 Cov.: 22

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1084709 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 356459

African (AFR) AF: 0.00 AC: 0 AN: 26031

American (AMR) AF: 0.00 AC: 0 AN: 34702

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18991

East Asian (EAS) AF: 0.00 AC: 0 AN: 29715

South Asian (SAS) AF: 0.00 AC: 0 AN: 53458

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 39709

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4077

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 832620

Other (OTH) AF: 0.00 AC: 0 AN: 45406

GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 112082 Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0 AN XY: 34872

African (AFR) AF: 0.00 AC: 0 AN: 30990

American (AMR) AF: 0.00 AC: 0 AN: 10657

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2635

East Asian (EAS) AF: 0.00 AC: 0 AN: 3599

South Asian (SAS) AF: 0.00 AC: 0 AN: 2782

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6160

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 219

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 52830

Other (OTH) AF: 0.00 AC: 0 AN: 1537

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.9
Mutation Taster		=54/46	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1256966146; hg19: chrX-135956612;