rs7157492

chr14-35258383-G-Achr14-35258383-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014672.4(PRORP):c.1276-8344G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 152,002 control chromosomes in the GnomAD database, including 45,323 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 0.77 (45323 hom., cov: 32)
• Consequence: PRORP NM_014672.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.362

Genes affected

PRORP (HGNC:19958): (protein only RNase P catalytic subunit) Enables ribonuclease P activity. Involved in mitochondrial tRNA 5'-end processing. Located in mitochondrion and nucleoplasm. Part of mitochondrial ribonuclease P complex. [provided by Alliance of Genome Resources, Apr 2022]

PRORP-PSMA6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRORP	NM_014672.4	c.1276-8344G>A		intron_variant		ENST00000534898.9
PRORP-PSMA6	NR_182666.1	n.1784-8344G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRORP	ENST00000534898.9	c.1276-8344G>A		intron_variant		1	NM_014672.4	P1

Frequencies

GnomAD3 genomes AF: 0.772 AC: 117195 AN: 151884 Hom.: 45277 Cov.: 32

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.772 AC: 117303 AN: 152002 Hom.: 45323 Cov.: 32 AF XY: 0.772 AC XY: 57377 AN XY: 74294

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.810

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.802

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.775

Alfa AF: 0.660 Hom.: 1826

Bravo AF: 0.781

Asia WGS AF: 0.781 AC: 2715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.9
Dann	Benign	0.28

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: rs7157492; hg19: chr14-35727589;