X-47147662-C-CCTGTGCT

Variant names:

• chrX-47147662-C-CCTGTGCT
• rs59650471
• NM_005676.5:c.17+165_17+171dupCTGTGCT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_005676.5(RBM10):​c.17+165_17+171dupCTGTGCT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.14 (1062 hom., 4663 hem., cov: 18)
• Consequence: RBM10 NM_005676.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.42
• Publications: 0 publications found

Genes affected

RBM10 (HGNC:9896): (RNA binding motif protein 10) This gene encodes a nuclear protein that belongs to a family proteins that contain an RNA-binding motif. The encoded protein associates with hnRNP proteins and may be involved in regulating alternative splicing. Defects in this gene are the cause of the X-linked recessive disorder, TARP syndrome. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Mar 2011]

RBM10 Gene-Disease associations (from GenCC):

• TARP syndrome

  Inheritance: XL Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant X-47147662-C-CCTGTGCT is Benign according to our data. Variant chrX-47147662-C-CCTGTGCT is described in ClinVar as Benign. ClinVar VariationId is 1278217.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005676.5. 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
	RBM10	NM_005676.5	MANE Select	c.17+165_17+171dupCTGTGCT		intron	N/A	NP_005667.2
	RBM10	NM_001204468.2		c.212+165_212+171dupCTGTGCT		intron	N/A	NP_001191397.1	P98175-5
	RBM10	NM_001440861.1		c.212+165_212+171dupCTGTGCT		intron	N/A	NP_001427790.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBM10	ENST00000377604.8	TSL:1 MANE Select	c.17+164_17+165insCTGTGCT		intron	N/A	ENSP00000366829.3	P98175-1
	RBM10	ENST00000329236.8	TSL:1	c.212+164_212+165insCTGTGCT		intron	N/A	ENSP00000328848.8	P98175-5
	RBM10	ENST00000628161.2	TSL:1	c.17+164_17+165insCTGTGCT		intron	N/A	ENSP00000486115.1	P98175-4

Frequencies

GnomAD3 genomes AF: 0.144 AC: 15924 AN: 110807 Hom.: 1062 Cov.: 18

Gnomad AFR AF: 0.0307

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.146

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.144 AC: 15929 AN: 110860 Hom.: 1062 Cov.: 18 AF XY: 0.141 AC XY: 4663 AN XY: 33120

African (AFR) AF: 0.0306 AC: 939 AN: 30681

American (AMR) AF: 0.161 AC: 1676 AN: 10398

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 747 AN: 2624

East Asian (EAS) AF: 0.153 AC: 536 AN: 3493

South Asian (SAS) AF: 0.130 AC: 345 AN: 2655

European-Finnish (FIN) AF: 0.245 AC: 1430 AN: 5835

Middle Eastern (MID) AF: 0.167 AC: 36 AN: 216

European-Non Finnish (NFE) AF: 0.188 AC: 9907 AN: 52757

Other (OTH) AF: 0.148 AC: 226 AN: 1523

Alfa AF: 0.174 Hom.: 906

Bravo AF: 0.139

Asia WGS AF: 0.165 AC: 417 AN: 2522

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs59650471; hg19: chrX-47007061;