Variant 1-12859755-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_023014.1(PRAMEF2):c.350C>G(p.Pro117Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.012 ( 22 hom., cov: 32)

Exomes 𝑓: 0.0016 ( 378 hom. )

Failed GnomAD Quality Control

Consequence

PRAMEF2
NM_023014.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0560

Variant links:

Genes affected

PRAMEF2 (HGNC:28841): (PRAME family member 2) Predicted to be involved in several processes, including negative regulation of apoptotic process; negative regulation of transcription, DNA-templated; and positive regulation of cell population proliferation. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

PRAMEF2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0074096024).

BP6

Variant 1-12859755-C-G is Benign according to our data. Variant chr1-12859755-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 3025684.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRAMEF2	NM_023014.1 linkuse as main transcript	c.350C>G	p.Pro117Arg	missense_variant	3/4	ENST00000240189.2	NP_075390.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRAMEF2	ENST00000240189.2 linkuse as main transcript	c.350C>G	p.Pro117Arg	missense_variant	3/4	1	NM_023014.1	ENSP00000240189	P1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

1788

AN:

146850

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00324

Gnomad AMI

AF:

0.00221

Gnomad AMR

AF:

0.0162

Gnomad ASJ

AF:

0.0136

Gnomad EAS

AF:

0.0164

Gnomad SAS

AF:

0.0283

Gnomad FIN

AF:

0.00871

Gnomad MID

AF:

0.00329

Gnomad NFE

AF:

0.0160

Gnomad OTH

AF:

0.0147

GnomAD3 exomes

AF:

0.000649

AC:

160

AN:

246482

Hom.:

AF XY:

0.000607

AC XY:

AN XY:

133400

show subpopulations

Gnomad AFR exome

AF:

0.0000626

Gnomad AMR exome

AF:

0.00105

Gnomad ASJ exome

AF:

0.000502

Gnomad EAS exome

AF:

0.00100

Gnomad SAS exome

AF:

0.00121

Gnomad FIN exome

AF:

0.0000464

Gnomad NFE exome

AF:

0.000518

Gnomad OTH exome

AF:

0.00100

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00157

AC:

2233

AN:

1421376

Hom.:

378

Cov.:

AF XY:

0.00179

AC XY:

1262

AN XY:

706074

show subpopulations

Gnomad4 AFR exome

AF:

0.000181

Gnomad4 AMR exome

AF:

0.00279

Gnomad4 ASJ exome

AF:

0.00157

Gnomad4 EAS exome

AF:

0.00485

Gnomad4 SAS exome

AF:

0.00624

Gnomad4 FIN exome

AF:

0.000687

Gnomad4 NFE exome

AF:

0.00114

Gnomad4 OTH exome

AF:

0.00164

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0122

AC:

1787

AN:

146948

Hom.:

Cov.:

AF XY:

0.0124

AC XY:

891

AN XY:

71706

show subpopulations

Gnomad4 AFR

AF:

0.00323

Gnomad4 AMR

AF:

0.0162

Gnomad4 ASJ

AF:

0.0136

Gnomad4 EAS

AF:

0.0165

Gnomad4 SAS

AF:

0.0281

Gnomad4 FIN

AF:

0.00871

Gnomad4 NFE

AF:

0.0160

Gnomad4 OTH

AF:

0.0150

Alfa

AF:

0.00895

Hom.:

ExAC

AF:

0.00243

AC:

295

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2024

PRAMEF2: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.24

BayesDel_noAF

Benign

-0.58

CADD

Benign

9.4

DANN

Benign

0.92

DEOGEN2

Benign

0.012

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.0016

M_CAP

Benign

0.0017

MetaRNN

Benign

0.0074

MetaSVM

Benign

-0.92

MutationAssessor

Benign

1.1

MutationTaster

Benign

1.0

PrimateAI

Uncertain

0.50

PROVEAN

Benign

-0.39

REVEL

Benign

0.028

Sift

Uncertain

0.015

Sift4G

Uncertain

0.0080

Polyphen

0.041

Vest4

0.11

MVP

0.13

MPC

0.055

ClinPred

0.0016

GERP RS

-0.29

Varity_R

0.038

gMVP

0.32

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over