Variant chrX-154398551-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006013.5(RPL10):c.23+9T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00433 in 1,209,684 control chromosomes in the GnomAD database, including 154 homozygotes. There are 1,507 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0053 ( 12 hom., 196 hem., cov: 24)

Exomes 𝑓: 0.0042 ( 142 hom. 1311 hem. )

Consequence

RPL10
NM_006013.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.974

Variant links:

Genes affected

RPL10 (HGNC:10298): (ribosomal protein L10) This gene encodes a ribosomal protein that is a component of the 60S ribosome subunit. The related protein in chicken can bind to c-Jun and can repress c-Jun-mediated transcriptional activation. Some studies have detected an association between variation in this gene and autism spectrum disorders, though others do not detect this relationship. There are multiple pseudogenes of this gene dispersed throughout the genome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

RPL10 links:

(HGNC:):

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=-0.71).

BP6

Variant X-154398551-T-A is Benign according to our data. Variant chrX-154398551-T-A is described in ClinVar as [Benign]. Clinvar id is 130161.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPL10	NM_006013.5 linkuse as main transcript	c.23+9T>A		intron_variant		ENST00000369817.7	NP_006004.3
LOC124905228	XR_007068356.1 linkuse as main transcript	n.292A>T		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPL10	ENST00000369817.7 linkuse as main transcript	c.23+9T>A		intron_variant		5	NM_006013.5	ENSP00000358832	P1
	ENST00000624054.2 linkuse as main transcript	n.292A>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.00524

AC:

589

AN:

112384

Hom.:

Cov.:

AF XY:

0.00562

AC XY:

194

AN XY:

34528

show subpopulations

Gnomad AFR

AF:

0.000420

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0395

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0346

Gnomad SAS

AF:

0.00219

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000244

Gnomad OTH

AF:

0.00794

GnomAD3 exomes

AF:

0.0156

AC:

2862

AN:

183045

Hom.:

104

AF XY:

0.0113

AC XY:

762

AN XY:

67531

show subpopulations

Gnomad AFR exome

AF:

0.000380

Gnomad AMR exome

AF:

0.0821

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0379

Gnomad SAS exome

AF:

0.000472

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000195

Gnomad OTH exome

AF:

0.0121

GnomAD4 exome

AF:

0.00423

AC:

4645

AN:

1097246

Hom.:

142

Cov.:

AF XY:

0.00361

AC XY:

1311

AN XY:

362818

show subpopulations

Gnomad4 AFR exome

AF:

0.000531

Gnomad4 AMR exome

AF:

0.0768

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0525

Gnomad4 SAS exome

AF:

0.000758

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000113

Gnomad4 OTH exome

AF:

0.00432

GnomAD4 genome

AF:

0.00532

AC:

598

AN:

112438

Hom.:

Cov.:

AF XY:

0.00567

AC XY:

196

AN XY:

34592

show subpopulations

Gnomad4 AFR

AF:

0.000419

Gnomad4 AMR

AF:

0.0402

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0347

Gnomad4 SAS

AF:

0.00256

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000244

Gnomad4 OTH

AF:

0.00784

Alfa

AF:

0.00365

Hom.:

Bravo

AF:

0.00961

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Feb 12, 2015	- -
Likely benign, no assertion criteria provided	clinical testing	Genetic Services Laboratory, University of Chicago	-	Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

1.0

DANN

Benign

0.68

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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