19-41860775-A-C

Position:

• chr19-41860775-A-C

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP5_Moderate

The NM_001022.4(RPS19):​c.1A>C​(p.Met1?) variant causes a start lost, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: RPS19 NM_001022.4 start_lost, splice_region
• Scores: Splicing: ADA: 0.3888
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 8.14

Genes affected

RPS19 (HGNC:10402): (ribosomal protein S19) 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 S19E family of ribosomal proteins. It is located in the cytoplasm. Mutations in this gene cause Diamond-Blackfan anemia (DBA), a constitutional erythroblastopenia characterized by absent or decreased erythroid precursors, in a subset of patients. This suggests a possible extra-ribosomal function for this gene in erythropoietic differentiation and proliferation, in addition to its ribosomal function. Higher expression levels of this gene in some primary colon carcinomas compared to matched normal colon tissues has been observed. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 19-41860775-A-C is Pathogenic according to our data. Variant chr19-41860775-A-C is described in ClinVar as [Pathogenic]. Clinvar id is 2780439.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPS19	NM_001022.4	c.1A>C	p.Met1?	start_lost, splice_region_variant	2/6	ENST00000598742.6	NP_001013.1
RPS19	NM_001321485.2	c.1A>C	p.Met1?	start_lost, splice_region_variant	2/6		NP_001308414.1
RPS19	NM_001321483.2	c.1A>C	p.Met1?	start_lost, splice_region_variant	2/6		NP_001308412.1
RPS19	NM_001321484.2	c.1A>C	p.Met1?	start_lost, splice_region_variant	2/6		NP_001308413.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPS19	ENST00000598742.6	c.1A>C	p.Met1?	start_lost, splice_region_variant	2/6	1	NM_001022.4	ENSP00000470972	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Diamond-Blackfan anemia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Oct 22, 2023

This sequence change affects the initiator methionine of the RPS19 mRNA. The next in-frame methionine is located at codon 75. This variant is not present in population databases (gnomAD no frequency). Disruption of the initiator codon has been observed in individuals with Diamond-Blackfan anemia (PMID: 24675553, 27329125, 28102861; Invitae). For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.58	D
BayesDel_noAF	Pathogenic	0.60
CADD	Uncertain	25
DANN	Benign	0.95
DEOGEN2	Uncertain	0.52	D;.;D;.;D
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.79
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.90	.;D;.;D;D
M_CAP	Pathogenic	0.94	D
MetaRNN	Pathogenic	0.99	D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationTaster	Benign	1.0	D
Sift4G	Uncertain	0.011	D;D;D;D;D
Polyphen		1.0	D;.;D;.;D
Vest4		0.95
MutPred		0.99		Gain of catalytic residue at M1 (P = 0.0986);Gain of catalytic residue at M1 (P = 0.0986);Gain of catalytic residue at M1 (P = 0.0986);Gain of catalytic residue at M1 (P = 0.0986);Gain of catalytic residue at M1 (P = 0.0986);
MVP		0.96
ClinPred		0.99	D
GERP RS		4.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.63
gMVP		0.52

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.39
dbscSNV1_RF	Benign	0.62
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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-42364845;