Variant rs12744840 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_184311.1(PEF1-AS1):n.296+654T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0434 in 153,428 control chromosomes in the GnomAD database, including 209 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 0.044 ( 209 hom., cov: 32)

Exomes 𝑓: 0.021 ( 0 hom. )

Consequence

PEF1-AS1
NR_184311.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.324

Variant links:

Genes affected

(HGNC:):

links:

PEF1-AS1 (HGNC:40154): (PEF1 and COL16A1 antisense RNA 1)

PEF1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
PEF1-AS1	NR_184311.1 linkuse as main transcript	n.296+654T>C	intron_variant, non_coding_transcript_variant
PEF1-AS1	NR_184312.1 linkuse as main transcript	n.296+654T>C	intron_variant, non_coding_transcript_variant
PEF1-AS1	NR_184313.1 linkuse as main transcript	n.296+654T>C	intron_variant, non_coding_transcript_variant
PEF1-AS1	NR_184314.1 linkuse as main transcript	n.326+118T>C	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000581333.1 linkuse as main transcript	n.153+654T>C		intron_variant, non_coding_transcript_variant		4
PEF1-AS1	ENST00000609549.5 linkuse as main transcript	n.248+1204T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.0436

AC:

6635

AN:

152122

Hom.:

209

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0116

Gnomad AMI

AF:

0.141

Gnomad AMR

AF:

0.0373

Gnomad ASJ

AF:

0.0311

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00580

Gnomad FIN

AF:

0.0619

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0672

Gnomad OTH

AF:

0.0412

GnomAD4 exome

AF:

0.0210

AC:

AN:

1188

Hom.:

AF XY:

0.0176

AC XY:

AN XY:

740

show subpopulations

Gnomad4 AMR exome

AF:

0.00617

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00725

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0452

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0436

AC:

6631

AN:

152240

Hom.:

209

Cov.:

AF XY:

0.0421

AC XY:

3131

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.0116

Gnomad4 AMR

AF:

0.0372

Gnomad4 ASJ

AF:

0.0311

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00560

Gnomad4 FIN

AF:

0.0619

Gnomad4 NFE

AF:

0.0672

Gnomad4 OTH

AF:

0.0408

Alfa

AF:

0.0604

Hom.:

Bravo

AF:

0.0404

Asia WGS

AF:

0.00577

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

DANN

Benign

0.75

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