rs61762302

chr19-41872047-G-Achr19-41872047-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001022.4(RPS19):c.*670G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00596 in 152,604 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0060 (5 hom., cov: 32)
  • Exomes 𝑓: 0.0042 (0 hom.)
• Consequence: RPS19 NM_001022.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.58

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00597 (909/152368) while in subpopulation NFE AF= 0.00979 (666/68036). AF 95% confidence interval is 0.00917. There are 5 homozygotes in gnomad4. There are 428 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High AC in GnomAd at 908 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RPS19	NM_001022.4	c.*670G>A		3_prime_UTR_variant	6/6	ENST00000598742.6
RPS19	NM_001321483.2	c.*670G>A		3_prime_UTR_variant	6/6
RPS19	NM_001321484.2	c.*670G>A		3_prime_UTR_variant	6/6
RPS19	NM_001321485.2	c.*650G>A		3_prime_UTR_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPS19	ENST00000598742.6	c.*670G>A		3_prime_UTR_variant	6/6	1	NM_001022.4	P1

Frequencies

GnomAD3 genomes AF: 0.00596 AC: 908 AN: 152250 Hom.: 5 Cov.: 32

Gnomad AFR AF: 0.00164

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.00608

Gnomad ASJ AF: 0.00605

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00103

Gnomad FIN AF: 0.00301

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00979

Gnomad OTH AF: 0.00718

GnomAD4 exome AF: 0.00424 AC: 1 AN: 236 Hom.: 0 Cov.: 0 AF XY: 0.00769 AC XY: 1 AN XY: 130

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00515

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00597 AC: 909 AN: 152368 Hom.: 5 Cov.: 32 AF XY: 0.00574 AC XY: 428 AN XY: 74516

Gnomad4 AFR AF: 0.00164

Gnomad4 AMR AF: 0.00608

Gnomad4 ASJ AF: 0.00605

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00103

Gnomad4 FIN AF: 0.00301

Gnomad4 NFE AF: 0.00979

Gnomad4 OTH AF: 0.00758

Alfa AF: 0.00305 Hom.: 0

Bravo AF: 0.00629

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.18
Dann	Benign	0.60

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: rs61762302; hg19: chr19-42376115;