Genetic Variant RNPEPL1:c.1510+225G>C (chr2-240575835-G-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_018226.6(RNPEPL1):c.1510+225G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

RNPEPL1
NM_018226.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.617

Publications

0 publications found

Variant links:

Genes affected

RNPEPL1 (HGNC:10079): (arginyl aminopeptidase like 1) Enables metalloaminopeptidase activity. Involved in proteolysis. [provided by Alliance of Genome Resources, Apr 2022]

RNPEPL1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RNPEPL1	NM_018226.6 link	c.1510+225G>C		intron_variant	Intron 8 of 10	ENST00000270357.10	NP_060696.4	Q9HAU8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RNPEPL1	ENST00000270357.10 link	c.1510+225G>C		intron_variant	Intron 8 of 10	1	NM_018226.6	ENSP00000270357.4		Q9HAU8

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

406178

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

213120

African (AFR)

AF:

0.00

AC:

AN:

11674

American (AMR)

AF:

0.00

AC:

AN:

17474

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

12570

East Asian (EAS)

AF:

0.00

AC:

AN:

29000

South Asian (SAS)

AF:

0.00

AC:

AN:

42018

European-Finnish (FIN)

AF:

0.00

AC:

AN:

26234

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1782

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

241728

Other (OTH)

AF:

0.00

AC:

AN:

23698

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.61

(source)

DANN

Benign

0.74

PhyloP100

-0.62

PromoterAI

-0.0034

Neutral

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over