NM_006413.5:c.432+1064G>T

Variant names:

• chr10-90886965-G-T
• rs4933617
• NM_006413.5:c.432+1064G>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.432+1064G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 150,244 control chromosomes in the GnomAD database, including 29,124 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 0.60 (29124 hom., cov: 27)
• Consequence: RPP30 NM_006413.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 2 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=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPP30	NM_006413.5	MANE Select	c.432+1064G>T		intron	N/A	NP_006404.1
	RPP30	NM_001104546.2		c.432+1064G>T		intron	N/A	NP_001098016.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPP30	ENST00000371703.8	TSL:1 MANE Select	c.432+1064G>T		intron	N/A	ENSP00000360768.3
	RPP30	ENST00000413330.5	TSL:5	c.432+1064G>T		intron	N/A	ENSP00000389182.1
	RPP30	ENST00000913126.1		c.453+1064G>T		intron	N/A	ENSP00000583185.1

Frequencies

GnomAD3 genomes AF: 0.600 AC: 90102 AN: 150126 Hom.: 29080 Cov.: 27

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.600 AC: 90200 AN: 150244 Hom.: 29124 Cov.: 27 AF XY: 0.596 AC XY: 43758 AN XY: 73390

African (AFR) AF: 0.866 AC: 35222 AN: 40684

American (AMR) AF: 0.543 AC: 8204 AN: 15104

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1691 AN: 3386

East Asian (EAS) AF: 0.451 AC: 2293 AN: 5086

South Asian (SAS) AF: 0.586 AC: 2788 AN: 4758

European-Finnish (FIN) AF: 0.425 AC: 4410 AN: 10380

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.501 AC: 33827 AN: 67562

Other (OTH) AF: 0.575 AC: 1200 AN: 2088

Alfa AF: 0.566 Hom.: 3246

Bravo AF: 0.619

Asia WGS AF: 0.515 AC: 1793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.39
DANN	Benign	0.20
PhyloP100		-1.1
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: rs4933617; hg19: chr10-92646722; COSMIC: COSV53295126;