dbSNP rs3792587: ENSG00000293259:n.232C>A (chr3-183885155-C-A) – 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 ENST00000445165.2(ENSG00000293259):n.232C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000263 in 379,906 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 32)

Exomes 𝑓: 0.0000026 ( 0 hom. )

Consequence

ENSG00000293259
ENST00000445165.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.535

Publications

0 publications found

Variant links:

Genes affected

ENSG00000293259 (HGNC:):

ENSG00000293259 links:

PARL (HGNC:18253): (presenilin associated rhomboid like) This gene encodes a member of the rhomboid family of intramembrane serine proteases that is localized to the inner mitochondrial membrane. The encoded protein regulates mitochondrial remodeling and apoptosis through regulated substrate proteolysis. Proteolytic processing of the encoded protein results in the release of a small peptide, P-beta, which may transit to the nucleus. Mutations in this gene may be associated with Parkinson's disease. [provided by RefSeq, May 2016]

PARL 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=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
ENSG00000293259	ENST00000445165.2 link	n.232C>A	non_coding_transcript_exon_variant	Exon 1 of 2	2
ENSG00000293259	ENST00000833400.1 link	n.119C>A	non_coding_transcript_exon_variant	Exon 1 of 2
PARL	ENST00000639100.1 link	c.-841G>T	upstream_gene_variant		5	ENSP00000491186.1	A0A1W2PP66

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000263

AC:

AN:

379906

Hom.:

Cov.:

AF XY:

0.00000502

AC XY:

AN XY:

199344

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

10990

American (AMR)

AF:

0.00

AC:

AN:

16400

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11772

East Asian (EAS)

AF:

0.00

AC:

AN:

25032

South Asian (SAS)

AF:

0.0000222

AC:

AN:

44962

European-Finnish (FIN)

AF:

0.00

AC:

AN:

23070

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1624

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

224134

Other (OTH)

AF:

0.00

AC:

AN:

21922

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

5.1

(source)

DANN

Benign

0.52

PhyloP100

-0.54

PromoterAI

0.020

Neutral

(source)

Splicing

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