10-90893362-C-T

Variant names:

• chr10-90893362-C-T
• rs10509613
• NM_006413.5:c.433-1413C>T

Variant summary

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

The NM_006413.5(RPP30):​c.433-1413C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 151,968 control chromosomes in the GnomAD database, including 12,061 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 0.37 (12061 hom., cov: 31)
• Consequence: RPP30 NM_006413.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 3 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPP30	NM_006413.5	c.433-1413C>T		intron_variant	Intron 6 of 10	ENST00000371703.8	NP_006404.1
RPP30	NM_001104546.2	c.433-1413C>T		intron_variant	Intron 6 of 13		NP_001098016.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPP30	ENST00000371703.8	c.433-1413C>T		intron_variant	Intron 6 of 10	1	NM_006413.5	ENSP00000360768.3

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56183 AN: 151850 Hom.: 12063 Cov.: 31

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.370 AC: 56187 AN: 151968 Hom.: 12061 Cov.: 31 AF XY: 0.372 AC XY: 27591 AN XY: 74242

African (AFR) AF: 0.130 AC: 5402 AN: 41484

American (AMR) AF: 0.456 AC: 6959 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1600 AN: 3472

East Asian (EAS) AF: 0.359 AC: 1856 AN: 5172

South Asian (SAS) AF: 0.408 AC: 1956 AN: 4798

European-Finnish (FIN) AF: 0.454 AC: 4775 AN: 10518

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32202 AN: 67954

Other (OTH) AF: 0.393 AC: 829 AN: 2110

Alfa AF: 0.289 Hom.: 873

Bravo AF: 0.360

Asia WGS AF: 0.368 AC: 1282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.8
DANN	Benign	0.67
PhyloP100		0.14
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: rs10509613; hg19: chr10-92653119;