X-47169510-G-T

Variant names:

• chrX-47169510-G-T
• rs367790106
• NM_005676.5:c.201+12G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_005676.5(RBM10):​c.201+12G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000922 in 1,084,800 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 24)
  • Exomes 𝑓: 9.2e-7 (0 hom. 0 hem.)
• Consequence: RBM10 NM_005676.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.02
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

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.201+12G>T		intron	N/A	NP_005667.2
	RBM10	NM_001204468.2		c.396+12G>T		intron	N/A	NP_001191397.1	P98175-5
	RBM10	NM_001440861.1		c.396+12G>T		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.201+12G>T		intron	N/A	ENSP00000366829.3	P98175-1
	RBM10	ENST00000329236.8	TSL:1	c.396+12G>T		intron	N/A	ENSP00000328848.8	P98175-5
	RBM10	ENST00000628161.2	TSL:1	c.201+12G>T		intron	N/A	ENSP00000486115.1	P98175-4

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome AF: 9.22e-7 AC: 1 AN: 1084800 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 352956

African (AFR) AF: 0.00 AC: 0 AN: 26174

American (AMR) AF: 0.00 AC: 0 AN: 33516

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19157

East Asian (EAS) AF: 0.00 AC: 0 AN: 29720

South Asian (SAS) AF: 0.00 AC: 0 AN: 52521

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 39192

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3295

European-Non Finnish (NFE) AF: 0.00000120 AC: 1 AN: 835639

Other (OTH) AF: 0.00 AC: 0 AN: 45586

GnomAD4 genome Cov.: 24

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.8
DANN	Benign	0.58
PhyloP100		3.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs367790106; hg19: chrX-47028909;