rs11021111

Variant names:

• chr11-95270099-C-G
• rs11021111
• ENST00000798492.1:n.1181-13908C>G

Variant summary

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

The ENST00000798492.1(LNCRNA-IUR):​n.1181-13908C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0454 in 152,236 control chromosomes in the GnomAD database, including 328 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 0.045 (328 hom., cov: 32)
• Consequence: LNCRNA-IUR ENST00000798492.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.542
• Publications: 1 publications found

Genes affected

LNCRNA-IUR (HGNC:55755): (lncRNA imatinib upregulated)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 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
LNCRNA-IUR	ENST00000798492.1	n.1181-13908C>G		intron_variant	Intron 2 of 4
LNCRNA-IUR	ENST00000798493.1	n.1158-39280C>G		intron_variant	Intron 2 of 2
LNCRNA-IUR	ENST00000798494.1	n.1656-13908C>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0453 AC: 6898 AN: 152118 Hom.: 326 Cov.: 32

Gnomad AFR AF: 0.0809

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0331

Gnomad ASJ AF: 0.00835

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.0774

Gnomad FIN AF: 0.0709

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0100

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0454 AC: 6909 AN: 152236 Hom.: 328 Cov.: 32 AF XY: 0.0493 AC XY: 3667 AN XY: 74420

African (AFR) AF: 0.0808 AC: 3359 AN: 41556

American (AMR) AF: 0.0334 AC: 511 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00835 AC: 29 AN: 3472

East Asian (EAS) AF: 0.215 AC: 1112 AN: 5172

South Asian (SAS) AF: 0.0763 AC: 368 AN: 4826

European-Finnish (FIN) AF: 0.0709 AC: 751 AN: 10588

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00998 AC: 679 AN: 68012

Other (OTH) AF: 0.0454 AC: 96 AN: 2114

Alfa AF: 0.0284 Hom.: 19

Bravo AF: 0.0432

Asia WGS AF: 0.163 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.8
DANN	Benign	0.34
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs11021111; hg19: chr11-95003263;