rs11224228

chr11-135070522-C-T

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02684	ENST00000532071.1	n.547+3592G>A		intron_variant, non_coding_transcript_variant		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;