Variant rs12803308 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_047481.2(JRKL-AS1):n.268A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 152,022 control chromosomes in the GnomAD database, including 36,795 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 0.69 ( 36775 hom., cov: 30)

Exomes 𝑓: 0.76 ( 20 hom. )

Consequence

JRKL-AS1
NR_047481.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.191

Variant links:

Genes affected

JRKL-AS1 (HGNC:43670): (JRKL antisense RNA 1)

JRKL-AS1 links:

JRKL (HGNC:6200): (JRK like) The function of this gene has not yet been defined, however, the encoded protein shares similarity with the human (41% identical) and mouse (34% identical) jerky gene products. This protein may act as a nuclear regulatory protein. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, May 2012]

JRKL links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JRKL-AS1	NR_047481.2 linkuse as main transcript	n.268A>T		non_coding_transcript_exon_variant	3/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
JRKL-AS1	ENST00000511243.2 linkuse as main transcript	n.218A>T		non_coding_transcript_exon_variant	3/4	2
JRKL	ENST00000546177.1 linkuse as main transcript	n.198+43054T>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.690

AC:

104704

AN:

151836

Hom.:

36740

Cov.:

show subpopulations

Gnomad AFR

AF:

0.796

Gnomad AMI

AF:

0.656

Gnomad AMR

AF:

0.617

Gnomad ASJ

AF:

0.765

Gnomad EAS

AF:

0.364

Gnomad SAS

AF:

0.587

Gnomad FIN

AF:

0.661

Gnomad MID

AF:

0.696

Gnomad NFE

AF:

0.674

Gnomad OTH

AF:

0.694

GnomAD4 exome

AF:

0.765

AC:

AN:

Hom.:

Cov.:

AF XY:

0.750

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 AMR exome

AF:

1.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.750

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.808

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.690

AC:

104798

AN:

151954

Hom.:

36775

Cov.:

AF XY:

0.685

AC XY:

50895

AN XY:

74246

show subpopulations

Gnomad4 AFR

AF:

0.796

Gnomad4 AMR

AF:

0.616

Gnomad4 ASJ

AF:

0.765

Gnomad4 EAS

AF:

0.364

Gnomad4 SAS

AF:

0.586

Gnomad4 FIN

AF:

0.661

Gnomad4 NFE

AF:

0.674

Gnomad4 OTH

AF:

0.693

Alfa

AF:

0.585

Hom.:

1855

Bravo

AF:

0.687

Asia WGS

AF:

0.535

AC:

1864

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.6

DANN

Benign

0.88

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