rs11223548

Variant names:

• chr11-133661760-C-T
• rs11223548
• ENST00000762255.1:n.379-7913G>A

Variant summary

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

The ENST00000762255.1(LINC02743):​n.379-7913G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0442 in 152,230 control chromosomes in the GnomAD database, including 480 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 0.044 (480 hom., cov: 32)
• Consequence: LINC02743 ENST00000762255.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760
• Publications: 2 publications found

Genes affected

LINC02743 (HGNC:54261): (long intergenic non-protein coding RNA 2743)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762255.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02743	ENST00000762255.1		n.379-7913G>A		intron	N/A
	LINC02743	ENST00000762256.1		n.389-7913G>A		intron	N/A
	LINC02743	ENST00000762257.1		n.403-7913G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0441 AC: 6714 AN: 152112 Hom.: 481 Cov.: 32

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0954

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.0488

Gnomad FIN AF: 0.00613

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00516

Gnomad OTH AF: 0.0397

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

GnomAD4 genome AF: 0.0442 AC: 6722 AN: 152230 Hom.: 480 Cov.: 32 AF XY: 0.0465 AC XY: 3461 AN XY: 74420

African (AFR) AF: 0.0696 AC: 2890 AN: 41530

American (AMR) AF: 0.0956 AC: 1462 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0112 AC: 39 AN: 3472

East Asian (EAS) AF: 0.309 AC: 1597 AN: 5164

South Asian (SAS) AF: 0.0484 AC: 233 AN: 4816

European-Finnish (FIN) AF: 0.00613 AC: 65 AN: 10608

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00516 AC: 351 AN: 68026

Other (OTH) AF: 0.0393 AC: 83 AN: 2112

Alfa AF: 0.0285 Hom.: 330

Bravo AF: 0.0538

Asia WGS AF: 0.141 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.35
DANN	Benign	0.42
PhyloP100		-0.076

Splicing

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

Other links and lift over

dbSNP: rs11223548; hg19: chr11-133531655;