Variant 1-12859030-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_023014.1(PRAMEF2):c.21G>C(p.Pro7=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000241 in 1,590,252 control chromosomes in the GnomAD database, including 55 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00068 ( 3 hom., cov: 31)

Exomes 𝑓: 0.00020 ( 52 hom. )

Consequence

PRAMEF2
NM_023014.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.85

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 Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BP6

Variant 1-12859030-G-C is Benign according to our data. Variant chr1-12859030-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 2638268.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.85 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRAMEF2	NM_023014.1 linkuse as main transcript	c.21G>C	p.Pro7=	synonymous_variant	2/4	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.21G>C	p.Pro7=	synonymous_variant	2/4	1	NM_023014.1	ENSP00000240189	P1

Frequencies

GnomAD3 genomes

AF:

0.000684

AC:

101

AN:

147764

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00103

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00147

Gnomad ASJ

AF:

0.000295

Gnomad EAS

AF:

0.00180

Gnomad SAS

AF:

0.000666

Gnomad FIN

AF:

0.000288

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000317

Gnomad OTH

AF:

0.000500

GnomAD3 exomes

AF:

0.00437

AC:

1026

AN:

234516

Hom.:

AF XY:

0.00429

AC XY:

545

AN XY:

127148

show subpopulations

Gnomad AFR exome

AF:

0.00233

Gnomad AMR exome

AF:

0.00622

Gnomad ASJ exome

AF:

0.00166

Gnomad EAS exome

AF:

0.0105

Gnomad SAS exome

AF:

0.00672

Gnomad FIN exome

AF:

0.000421

Gnomad NFE exome

AF:

0.00351

Gnomad OTH exome

AF:

0.00606

GnomAD4 exome

AF:

0.000196

AC:

282

AN:

1442384

Hom.:

Cov.:

AF XY:

0.000219

AC XY:

157

AN XY:

717126

show subpopulations

Gnomad4 AFR exome

AF:

0.00127

Gnomad4 AMR exome

AF:

0.000377

Gnomad4 ASJ exome

AF:

0.000350

Gnomad4 EAS exome

AF:

0.000491

Gnomad4 SAS exome

AF:

0.000644

Gnomad4 FIN exome

AF:

0.0000377

Gnomad4 NFE exome

AF:

0.000103

Gnomad4 OTH exome

AF:

0.000387

GnomAD4 genome

AF:

0.000683

AC:

101

AN:

147868

Hom.:

Cov.:

AF XY:

0.000623

AC XY:

AN XY:

72200

show subpopulations

Gnomad4 AFR

AF:

0.00103

Gnomad4 AMR

AF:

0.00147

Gnomad4 ASJ

AF:

0.000295

Gnomad4 EAS

AF:

0.00181

Gnomad4 SAS

AF:

0.000666

Gnomad4 FIN

AF:

0.000288

Gnomad4 NFE

AF:

0.000317

Gnomad4 OTH

AF:

0.000495

Alfa

AF:

0.00849

Hom.:

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

May 01, 2022

PRAMEF2: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

2.4

DANN

Benign

0.37

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

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