Variant X-154398397-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_006013.5(RPL10):c.-24+3G>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 886,049 control chromosomes in the GnomAD database, including 6,838 homozygotes. There are 35,176 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 1814 hom., 6157 hem., cov: 25)

Exomes 𝑓: 0.13 ( 5024 hom. 29019 hem. )

Consequence

RPL10
NM_006013.5 splice_donor_region, intron

Scores

Splicing: ADA: 0.0003592

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.95

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 -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.28).

BP6

Variant X-154398397-G-A is Benign according to our data. Variant chrX-154398397-G-A is described in ClinVar as [Benign]. Clinvar id is 1327969.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 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.-24+3G>A		splice_donor_region_variant, intron_variant		ENST00000369817.7	NP_006004.3
LOC124905228	XR_007068356.1 linkuse as main transcript	n.446C>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.-24+3G>A		splice_donor_region_variant, intron_variant		5	NM_006013.5	ENSP00000358832	P1
	ENST00000624054.2 linkuse as main transcript	n.446C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.180

AC:

20347

AN:

112892

Hom.:

1802

Cov.:

AF XY:

0.175

AC XY:

6125

AN XY:

35062

show subpopulations

Gnomad AFR

AF:

0.341

Gnomad AMI

AF:

0.00730

Gnomad AMR

AF:

0.172

Gnomad ASJ

AF:

0.0549

Gnomad EAS

AF:

0.0933

Gnomad SAS

AF:

0.164

Gnomad FIN

AF:

0.143

Gnomad MID

AF:

0.0625

Gnomad NFE

AF:

0.109

Gnomad OTH

AF:

0.168

GnomAD3 exomes

AF:

0.144

AC:

25761

AN:

179374

Hom.:

1588

AF XY:

0.136

AC XY:

8947

AN XY:

65634

show subpopulations

Gnomad AFR exome

AF:

0.351

Gnomad AMR exome

AF:

0.201

Gnomad ASJ exome

AF:

0.0559

Gnomad EAS exome

AF:

0.0708

Gnomad SAS exome

AF:

0.166

Gnomad FIN exome

AF:

0.152

Gnomad NFE exome

AF:

0.107

Gnomad OTH exome

AF:

0.116

GnomAD4 exome

AF:

0.127

AC:

97883

AN:

773104

Hom.:

5024

Cov.:

AF XY:

0.130

AC XY:

29019

AN XY:

223062

show subpopulations

Gnomad4 AFR exome

AF:

0.343

Gnomad4 AMR exome

AF:

0.197

Gnomad4 ASJ exome

AF:

0.0600

Gnomad4 EAS exome

AF:

0.107

Gnomad4 SAS exome

AF:

0.171

Gnomad4 FIN exome

AF:

0.148

Gnomad4 NFE exome

AF:

0.112

Gnomad4 OTH exome

AF:

0.134

GnomAD4 genome

AF:

0.181

AC:

20407

AN:

112945

Hom.:

1814

Cov.:

AF XY:

0.175

AC XY:

6157

AN XY:

35125

show subpopulations

Gnomad4 AFR

AF:

0.341

Gnomad4 AMR

AF:

0.172

Gnomad4 ASJ

AF:

0.0549

Gnomad4 EAS

AF:

0.0925

Gnomad4 SAS

AF:

0.164

Gnomad4 FIN

AF:

0.143

Gnomad4 NFE

AF:

0.109

Gnomad4 OTH

AF:

0.179

Alfa

AF:

0.129

Hom.:

2808

Bravo

AF:

0.192

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Intellectual disability, X-linked, syndromic, 35

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Nov 07, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.28

CADD

Benign

DANN

Benign

0.92

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00036

dbscSNV1_RF

Benign

0.054

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