chr6-34418142-G-GT

Position:

• chr6-34418142-G-GT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001014.5(RPS10):​c.456+226_456+227insA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00332 in 1,456,772 control chromosomes in the GnomAD database, including 104 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.016 (52 hom., cov: 32)
  • Exomes 𝑓: 0.0019 (52 hom.)
• Consequence: RPS10 NM_001014.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0300

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-NUDT3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 6-34418142-G-GT is Benign according to our data. Variant chr6-34418142-G-GT is described in ClinVar as [Benign]. Clinvar id is 1228151.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPS10	NM_001014.5	c.456+226_456+227insA		intron_variant		ENST00000648437.1	NP_001005.1
RPS10-NUDT3	NM_001202470.3	c.456+226_456+227insA		intron_variant			NP_001189399.1
RPS10	NM_001203245.3	c.456+226_456+227insA		intron_variant			NP_001190174.1
RPS10	NM_001204091.2	c.456+226_456+227insA		intron_variant			NP_001191020.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPS10	ENST00000648437.1	c.456+226_456+227insA		intron_variant			NM_001014.5	ENSP00000497917	P1

Frequencies

GnomAD3 genomes AF: 0.0155 AC: 2358 AN: 152122 Hom.: 53 Cov.: 32

Gnomad AFR AF: 0.0517

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00799

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000794

Gnomad OTH AF: 0.0148

GnomAD4 exome AF: 0.00190 AC: 2476 AN: 1304532 Hom.: 52 Cov.: 28 AF XY: 0.00181 AC XY: 1150 AN XY: 635594

Gnomad4 AFR exome AF: 0.0527

Gnomad4 AMR exome AF: 0.00647

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000317

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000485

Gnomad4 OTH exome AF: 0.00520

GnomAD4 genome AF: 0.0155 AC: 2360 AN: 152240 Hom.: 52 Cov.: 32 AF XY: 0.0146 AC XY: 1086 AN XY: 74428

Gnomad4 AFR AF: 0.0516

Gnomad4 AMR AF: 0.00798

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00145

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000794

Gnomad4 OTH AF: 0.0147

Bravo AF: 0.0179

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 21, 2018

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs201724991; hg19: chr6-34385919;