rs11224228

Variant names:

• chr11-135070522-C-T
• rs11224228
• ENST00000532071.1:n.547+3592G>A

Variant summary

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

The ENST00000532071.1(LINC02684):​n.547+3592G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,028 control chromosomes in the GnomAD database, including 2,950 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 0.19 (2950 hom., cov: 32)
• Consequence: LINC02684 ENST00000532071.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.436

Genes affected

LINC02684 (HGNC:54180): (long intergenic non-protein coding RNA 2684)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 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
LINC02684	ENST00000532071.1	n.547+3592G>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29210 AN: 151910 Hom.: 2942 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.192 AC: 29240 AN: 152028 Hom.: 2950 Cov.: 32 AF XY: 0.192 AC XY: 14243 AN XY: 74320

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.176

Alfa AF: 0.166 Hom.: 1031

Bravo AF: 0.194

Asia WGS AF: 0.210 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.6
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11224228; hg19: chr11-134940416;