Variant chr1-12777491-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001080830.5(PRAMEF12):c.1344A>T(p.Ile448=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 1,613,250 control chromosomes in the GnomAD database, including 33,725 homozygotes. 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: 𝑓 0.29 ( 8356 hom., cov: 32)

Exomes 𝑓: 0.20 ( 25369 hom. )

Consequence

PRAMEF12
NM_001080830.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.38

Variant links:

Genes affected

PRAMEF12 (HGNC:22125): (PRAME family member 12) 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]

PRAMEF12 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.15).

BP7

Synonymous conserved (PhyloP=-5.38 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRAMEF12	NM_001080830.5 linkuse as main transcript	c.1344A>T	p.Ile448=	synonymous_variant	3/3	ENST00000357726.5	NP_001074299.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRAMEF12	ENST00000357726.5 linkuse as main transcript	c.1344A>T	p.Ile448=	synonymous_variant	3/3	2	NM_001080830.5	ENSP00000350358	P1

Frequencies

GnomAD3 genomes

AF:

0.294

AC:

44626

AN:

151686

Hom.:

8319

Cov.:

show subpopulations

Gnomad AFR

AF:

0.568

Gnomad AMI

AF:

0.0450

Gnomad AMR

AF:

0.204

Gnomad ASJ

AF:

0.133

Gnomad EAS

AF:

0.255

Gnomad SAS

AF:

0.220

Gnomad FIN

AF:

0.211

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.182

Gnomad OTH

AF:

0.263

GnomAD4 exome

AF:

0.201

AC:

293337

AN:

1461446

Hom.:

25369

Cov.:

AF XY:

0.200

AC XY:

145513

AN XY:

727008

show subpopulations

Gnomad4 AFR exome

AF:

0.581

Gnomad4 AMR exome

AF:

0.165

Gnomad4 ASJ exome

AF:

0.136

Gnomad4 EAS exome

AF:

0.250

Gnomad4 SAS exome

AF:

0.224

Gnomad4 FIN exome

AF:

0.215

Gnomad4 NFE exome

AF:

0.187

Gnomad4 OTH exome

AF:

0.219

GnomAD4 genome

AF:

0.295

AC:

44718

AN:

151804

Hom.:

8356

Cov.:

AF XY:

0.293

AC XY:

21764

AN XY:

74180

show subpopulations

Gnomad4 AFR

AF:

0.569

Gnomad4 AMR

AF:

0.203

Gnomad4 ASJ

AF:

0.133

Gnomad4 EAS

AF:

0.255

Gnomad4 SAS

AF:

0.221

Gnomad4 FIN

AF:

0.211

Gnomad4 NFE

AF:

0.182

Gnomad4 OTH

AF:

0.264

Alfa

AF:

0.187

Hom.:

1736

Bravo

AF:

0.316

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.11

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over