rs10501853

Variant names:

• chr11-96426102-G-A
• rs10501853
• ENST00000546177.1:n.198+21711G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000546177.1(JRKL):​n.198+21711G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 0 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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JRKL	ENST00000546177.1	n.198+21711G>A		intron_variant	Intron 2 of 2	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

African (AFR) AF: 0.767 AC: 31787 AN: 41440

American (AMR) AF: 0.580 AC: 8860 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2555 AN: 3468

East Asian (EAS) AF: 0.359 AC: 1855 AN: 5164

South Asian (SAS) AF: 0.556 AC: 2671 AN: 4804

European-Finnish (FIN) AF: 0.657 AC: 6905 AN: 10514

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46097 AN: 67954

Other (OTH) AF: 0.682 AC: 1440 AN: 2112

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10501853; hg19: chr11-96159266;