rs11224228

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.269 AC: 11126 AN: 41416

American (AMR) AF: 0.165 AC: 2526 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 374 AN: 3470

East Asian (EAS) AF: 0.192 AC: 989 AN: 5160

South Asian (SAS) AF: 0.177 AC: 855 AN: 4820

European-Finnish (FIN) AF: 0.179 AC: 1896 AN: 10584

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10925 AN: 67974

Other (OTH) AF: 0.176 AC: 371 AN: 2108

Alfa AF: 0.165 Hom.: 1147

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
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs11224228; hg19: chr11-134940416;