Variant chrX-47169518-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_005676.5(RBM10):c.201+20C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00119 in 1,193,164 control chromosomes in the GnomAD database, including 13 homozygotes. There are 755 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.00066 ( 1 hom., 37 hem., cov: 23)

Exomes 𝑓: 0.0012 ( 12 hom. 718 hem. )

Consequence

RBM10
NM_005676.5 intron

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0480

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant X-47169518-C-T is Benign according to our data. Variant chrX-47169518-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 445371.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000655 (74/112963) while in subpopulation SAS AF= 0.0259 (71/2742). AF 95% confidence interval is 0.0211. There are 1 homozygotes in gnomad4. There are 37 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.

BS2

High Hemizygotes in GnomAd4 at 37 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBM10	NM_005676.5 linkuse as main transcript	c.201+20C>T		intron_variant		ENST00000377604.8	NP_005667.2	P98175-1A0A0S2Z4W4

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
RBM10	ENST00000377604.8 linkuse as main transcript	c.201+20C>T	intron_variant	1	NM_005676.5	ENSP00000366829.3	P98175-1
RBM10	ENST00000329236.8 linkuse as main transcript	c.396+20C>T	intron_variant	1		ENSP00000328848.8	P98175-5
RBM10	ENST00000628161.2 linkuse as main transcript	c.201+20C>T	intron_variant	1		ENSP00000486115.1	P98175-4
RBM10	ENST00000345781.10 linkuse as main transcript	c.201+20C>T	intron_variant	2		ENSP00000329659.6	P98175-3

Frequencies

GnomAD3 genomes

AF:

0.000664

AC:

AN:

112910

Hom.:

Cov.:

AF XY:

0.00108

AC XY:

AN XY:

35054

show subpopulations

Gnomad AFR

AF:

0.0000642

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0262

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000188

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00291

AC:

438

AN:

150327

Hom.:

AF XY:

0.00490

AC XY:

223

AN XY:

45479

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000255

Gnomad SAS exome

AF:

0.0262

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00231

GnomAD4 exome

AF:

0.00125

AC:

1349

AN:

1080201

Hom.:

Cov.:

AF XY:

0.00205

AC XY:

718

AN XY:

350163

show subpopulations

Gnomad4 AFR exome

AF:

0.0000383

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000339

Gnomad4 SAS exome

AF:

0.0239

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000240

Gnomad4 OTH exome

AF:

0.00167

GnomAD4 genome

AF:

0.000655

AC:

AN:

112963

Hom.:

Cov.:

AF XY:

0.00105

AC XY:

AN XY:

35117

show subpopulations

Gnomad4 AFR

AF:

0.0000641

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0259

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000188

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000217

Hom.:

Bravo

AF:

0.000155

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 22, 2024	- -
Likely benign, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	May 11, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.2

DANN

Benign

0.55

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

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