Variant chr14-49583678-G-GA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001032.5(RPS29):c.163-4dupT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0756 in 1,010,158 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.00041 ( 0 hom., cov: 32)

Exomes 𝑓: 0.088 ( 0 hom. )

Consequence

RPS29
NM_001032.5 splice_region, intron

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: 0.536

Variant links:

Genes affected

RPS29 (HGNC:10419): (ribosomal protein S29) 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 and a member of the S14P family of ribosomal proteins. The protein, which contains a C2-C2 zinc finger-like domain that can bind to zinc, can enhance the tumor suppressor activity of Ras-related protein 1A (KREV1). 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. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2013]

RPS29 links:

RPS29 (HGNC:):

RPS29 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 14-49583678-G-GA is Benign according to our data. Variant chr14-49583678-G-GA is described in ClinVar as [Benign]. Clinvar id is 1248271.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
RPS29	NM_001032.5 linkuse as main transcript	c.163-4dupT	splice_region_variant, intron_variant	ENST00000245458.11	NP_001023.1	P62273-1
RPS29	NM_001030001.4 linkuse as main transcript	c.162+2271dupT	intron_variant		NP_001025172.1	P62273-2
RPS29	NM_001351375.2 linkuse as main transcript	c.154-4dupT	splice_region_variant, intron_variant		NP_001338304.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPS29	ENST00000245458.11 linkuse as main transcript	c.163-4dupT		splice_region_variant, intron_variant		1	NM_001032.5	ENSP00000245458.7		P62273-1

Frequencies

GnomAD3 genomes

AF:

0.000405

AC:

AN:

138168

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000213

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000218

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00216

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000426

Gnomad OTH

AF:

0.000532

GnomAD3 exomes

AF:

0.0964

AC:

8522

AN:

88432

Hom.:

AF XY:

0.0957

AC XY:

4548

AN XY:

47522

show subpopulations

Gnomad AFR exome

AF:

0.0803

Gnomad AMR exome

AF:

0.151

Gnomad ASJ exome

AF:

0.150

Gnomad EAS exome

AF:

0.123

Gnomad SAS exome

AF:

0.132

Gnomad FIN exome

AF:

0.0321

Gnomad NFE exome

AF:

0.0831

Gnomad OTH exome

AF:

0.130

GnomAD4 exome

AF:

0.0875

AC:

76299

AN:

871940

Hom.:

Cov.:

AF XY:

0.0884

AC XY:

38063

AN XY:

430436

show subpopulations

Gnomad4 AFR exome

AF:

0.0902

Gnomad4 AMR exome

AF:

0.0945

Gnomad4 ASJ exome

AF:

0.106

Gnomad4 EAS exome

AF:

0.104

Gnomad4 SAS exome

AF:

0.109

Gnomad4 FIN exome

AF:

0.0700

Gnomad4 NFE exome

AF:

0.0855

Gnomad4 OTH exome

AF:

0.0938

GnomAD4 genome

AF:

0.000405

AC:

AN:

138218

Hom.:

Cov.:

AF XY:

0.000360

AC XY:

AN XY:

66684

show subpopulations

Gnomad4 AFR

AF:

0.000212

Gnomad4 AMR

AF:

0.000218

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00216

Gnomad4 NFE

AF:

0.000426

Gnomad4 OTH

AF:

0.000529

ClinVar

Significance: 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	GeneDx	Aug 06, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 05, 2023	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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