rs10501853

Positions:

• chr11-96426102-G-A
• chr11-96426102-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000546177.1(JRKL):​n.198+21711G>A 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 0.678 in 151,928 control chromosomes in the GnomAD database, including 35,538 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 0.68 (35538 hom., cov: 30)
• Consequence: JRKL ENST00000546177.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
JRKL	ENST00000546177.1	n.198+21711G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102915 AN: 151808 Hom.: 35505 Cov.: 30

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.684

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.678 AC: 103003 AN: 151928 Hom.: 35538 Cov.: 30 AF XY: 0.673 AC XY: 49943 AN XY: 74248

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.682

Alfa AF: 0.552 Hom.: 2346

Bravo AF: 0.673

Asia WGS AF: 0.515 AC: 1785 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.52
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501853; hg19: chr11-96159266;