X-47147662-C-CCTGTGCT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_005676.5(RBM10):c.17+165_17+171dup 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

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]

ACMG classification

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBM10	NM_005676.5	c.17+165_17+171dup		intron_variant		ENST00000377604.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBM10	ENST00000377604.8	c.17+165_17+171dup		intron_variant		1	NM_005676.5	A1
RBM10	ENST00000329236.8	c.212+165_212+171dup		intron_variant		1		P3
RBM10	ENST00000628161.2	c.17+165_17+171dup		intron_variant		1
RBM10	ENST00000345781.10	c.17+165_17+171dup		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.144 AC: 15924 AN: 110807 Hom.: 1062 Cov.: 18 AF XY: 0.141 AC XY: 4652 AN XY: 33057

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

Gnomad4 AFR AF: 0.0306

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.148

Alfa AF: 0.174 Hom.: 906

Bravo AF: 0.139

Asia WGS AF: 0.165 AC: 417 AN: 2522

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 14, 2018

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs59650471; hg19: chrX-47007061;