Variant 1-12859771-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The ENST00000240189.2(PRAMEF2):c.366G>T(p.Leu122=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.011 ( 16 hom., cov: 32)

Exomes 𝑓: 0.0017 ( 503 hom. )

Failed GnomAD Quality Control

Consequence

PRAMEF2
ENST00000240189.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.734

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 -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BP6

Variant 1-12859771-G-T is Benign according to our data. Variant chr1-12859771-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 3025476.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.734 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRAMEF2	NM_023014.1 linkuse as main transcript	c.366G>T	p.Leu122=	synonymous_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.366G>T	p.Leu122=	synonymous_variant	3/4	1	NM_023014.1	ENSP00000240189	P1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

1624

AN:

146778

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00272

Gnomad AMI

AF:

0.00330

Gnomad AMR

AF:

0.0152

Gnomad ASJ

AF:

0.0124

Gnomad EAS

AF:

0.0168

Gnomad SAS

AF:

0.0259

Gnomad FIN

AF:

0.00773

Gnomad MID

AF:

0.00654

Gnomad NFE

AF:

0.0145

Gnomad OTH

AF:

0.0112

GnomAD3 exomes

AF:

0.000669

AC:

165

AN:

246514

Hom.:

AF XY:

0.000683

AC XY:

AN XY:

133282

show subpopulations

Gnomad AFR exome

AF:

0.000124

Gnomad AMR exome

AF:

0.00108

Gnomad ASJ exome

AF:

0.000302

Gnomad EAS exome

AF:

0.000891

Gnomad SAS exome

AF:

0.00142

Gnomad FIN exome

AF:

0.0000464

Gnomad NFE exome

AF:

0.000527

Gnomad OTH exome

AF:

0.00100

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00167

AC:

2362

AN:

1417350

Hom.:

503

Cov.:

AF XY:

0.00185

AC XY:

1303

AN XY:

703952

show subpopulations

Gnomad4 AFR exome

AF:

0.000241

Gnomad4 AMR exome

AF:

0.00294

Gnomad4 ASJ exome

AF:

0.00157

Gnomad4 EAS exome

AF:

0.00496

Gnomad4 SAS exome

AF:

0.00589

Gnomad4 FIN exome

AF:

0.000610

Gnomad4 NFE exome

AF:

0.00128

Gnomad4 OTH exome

AF:

0.00175

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0111

AC:

1623

AN:

146878

Hom.:

Cov.:

AF XY:

0.0113

AC XY:

807

AN XY:

71700

show subpopulations

Gnomad4 AFR

AF:

0.00271

Gnomad4 AMR

AF:

0.0152

Gnomad4 ASJ

AF:

0.0124

Gnomad4 EAS

AF:

0.0168

Gnomad4 SAS

AF:

0.0257

Gnomad4 FIN

AF:

0.00773

Gnomad4 NFE

AF:

0.0145

Gnomad4 OTH

AF:

0.0116

Alfa

AF:

0.00723

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

Jan 01, 2024

PRAMEF2: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.0

DANN

Benign

0.46

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