rs12803308

Variant names:

• chr11-96447445-T-A
• rs12803308
• ENST00000546177.1:n.198+43054T>A

Your query was ambiguous. Multiple possible variants found:

• chr11-96447445-T-A
• chr11-96447445-T-C
• chr11-96447445-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000546177.1(JRKL):​n.198+43054T>A variant causes a intron 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 ENST00000546177.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191
• Publications: 4 publications found

Genes affected

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

LINC02737 (HGNC:54254): (long intergenic non-protein coding RNA 2737)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
JRKL-AS1	NR_047481.2	n.268A>T		non_coding_transcript_exon_variant	Exon 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JRKL	ENST00000546177.1	n.198+43054T>A		intron_variant	Intron 2 of 2	1
JRKL-AS1	ENST00000511243.2	n.218A>T		non_coding_transcript_exon_variant	Exon 3 of 4	2
LINC02737	ENST00000716804.1	n.79+2737T>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104704 AN: 151836 Hom.: 36740 Cov.: 30

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: 52 AN: 68 Hom.: 20 Cov.: 0 AF XY: 0.750 AC XY: 42 AN XY: 56

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.750 AC: 3 AN: 4

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.808 AC: 42 AN: 52

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.690 AC: 104798 AN: 151954 Hom.: 36775 Cov.: 30 AF XY: 0.685 AC XY: 50895 AN XY: 74246

African (AFR) AF: 0.796 AC: 32967 AN: 41416

American (AMR) AF: 0.616 AC: 9412 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2655 AN: 3472

East Asian (EAS) AF: 0.364 AC: 1875 AN: 5158

South Asian (SAS) AF: 0.586 AC: 2822 AN: 4816

European-Finnish (FIN) AF: 0.661 AC: 6964 AN: 10538

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.674 AC: 45839 AN: 67962

Other (OTH) AF: 0.693 AC: 1463 AN: 2110

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
PhyloP100		0.19

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12803308; hg19: chr11-96180609;