rs4933620

Variant names:

• chr10-90900108-T-C
• rs4933620
• NM_006413.5:c.698-462T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006413.5(RPP30):​c.698-462T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,154 control chromosomes in the GnomAD database, including 4,122 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 0.21 (4122 hom., cov: 33)
• Consequence: RPP30 NM_006413.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 4 publications found

Genes affected

RPP30 (HGNC:17688): (ribonuclease P/MRP subunit p30) Enables ribonuclease P RNA binding activity. Contributes to ribonuclease P activity. Involved in tRNA 5'-leader removal. Part of multimeric ribonuclease P complex and ribonuclease MRP complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006413.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPP30	NM_006413.5	MANE Select	c.698-462T>C		intron	N/A	NP_006404.1
	RPP30	NM_001104546.2		c.698-462T>C		intron	N/A	NP_001098016.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPP30	ENST00000371703.8	TSL:1 MANE Select	c.698-462T>C		intron	N/A	ENSP00000360768.3
	RPP30	ENST00000413330.5	TSL:5	c.698-462T>C		intron	N/A	ENSP00000389182.1
	RPP30	ENST00000414836.1	TSL:3	c.530-462T>C		intron	N/A	ENSP00000407972.1

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31571 AN: 152036 Hom.: 4114 Cov.: 33

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.230

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.208 AC: 31603 AN: 152154 Hom.: 4122 Cov.: 33 AF XY: 0.209 AC XY: 15553 AN XY: 74384

African (AFR) AF: 0.358 AC: 14835 AN: 41488

American (AMR) AF: 0.224 AC: 3430 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3472

East Asian (EAS) AF: 0.281 AC: 1451 AN: 5172

South Asian (SAS) AF: 0.230 AC: 1109 AN: 4812

European-Finnish (FIN) AF: 0.122 AC: 1291 AN: 10606

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8312 AN: 68002

Other (OTH) AF: 0.228 AC: 481 AN: 2112

Alfa AF: 0.184 Hom.: 585

Bravo AF: 0.225

Asia WGS AF: 0.235 AC: 816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.49
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4933620; hg19: chr10-92659865;