Variant 6-34417740-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001014.5(RPS10):c.457-193T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 722,614 control chromosomes in the GnomAD database, including 9,640 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.087 ( 1332 hom., cov: 32)

Exomes 𝑓: 0.11 ( 8308 hom. )

Consequence

RPS10
NM_001014.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.260

Variant links:

Genes affected

RPS10 (HGNC:10383): (ribosomal protein S10) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 40S subunit. The protein belongs to the S10E family of ribosomal proteins. It is located in the cytoplasm. Variable expression of this gene in colorectal cancers compared to adjacent normal tissues has been observed, although no correlation between the level of expression and the severity of the disease has been found. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Alternate splicing results in multiple transcript variants that encode the same protein. Naturally occurring read-through transcription occurs between this locus and the neighboring locus NUDT3 (nudix (nucleoside diphosphate linked moiety X)-type motif 3).[provided by RefSeq, Feb 2011]

RPS10 links:

RPS10-NUDT3 (HGNC:):

RPS10-NUDT3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 6-34417740-A-T is Benign according to our data. Variant chr6-34417740-A-T is described in ClinVar as [Benign]. Clinvar id is 1178824.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
RPS10	NM_001014.5 linkuse as main transcript	c.457-193T>A	intron_variant	ENST00000648437.1	NP_001005.1
RPS10-NUDT3	NM_001202470.3 linkuse as main transcript	c.456+629T>A	intron_variant		NP_001189399.1
RPS10	NM_001203245.3 linkuse as main transcript	c.457-193T>A	intron_variant		NP_001190174.1
RPS10	NM_001204091.2 linkuse as main transcript	c.457-193T>A	intron_variant		NP_001191020.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPS10	ENST00000648437.1 linkuse as main transcript	c.457-193T>A		intron_variant			NM_001014.5	ENSP00000497917	P1

Frequencies

GnomAD3 genomes

AF:

0.0874

AC:

13287

AN:

152062

Hom.:

1324

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0592

Gnomad AMI

AF:

0.0888

Gnomad AMR

AF:

0.225

Gnomad ASJ

AF:

0.0718

Gnomad EAS

AF:

0.443

Gnomad SAS

AF:

0.204

Gnomad FIN

AF:

0.0799

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0400

Gnomad OTH

AF:

0.0989

GnomAD4 exome

AF:

0.107

AC:

61015

AN:

570434

Hom.:

8308

Cov.:

AF XY:

0.107

AC XY:

32941

AN XY:

307098

show subpopulations

Gnomad4 AFR exome

AF:

0.0582

Gnomad4 AMR exome

AF:

0.346

Gnomad4 ASJ exome

AF:

0.0607

Gnomad4 EAS exome

AF:

0.503

Gnomad4 SAS exome

AF:

0.178

Gnomad4 FIN exome

AF:

0.0799

Gnomad4 NFE exome

AF:

0.0395

Gnomad4 OTH exome

AF:

0.0944

GnomAD4 genome

AF:

0.0874

AC:

13300

AN:

152180

Hom.:

1332

Cov.:

AF XY:

0.0949

AC XY:

7065

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.0592

Gnomad4 AMR

AF:

0.226

Gnomad4 ASJ

AF:

0.0718

Gnomad4 EAS

AF:

0.443

Gnomad4 SAS

AF:

0.203

Gnomad4 FIN

AF:

0.0799

Gnomad4 NFE

AF:

0.0400

Gnomad4 OTH

AF:

0.0989

Alfa

AF:

0.0597

Hom.:

Bravo

AF:

0.102

Asia WGS

AF:

0.291

AC:

1009

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 17, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.73

DANN

Benign

0.45

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