rs2723603

Variant names:

• chr11-133799492-G-A
• rs2723603
• ENST00000526254.1:n.121+10585C>T

Variant summary

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

The NR_120444.1(LINC02743):​n.121+10585C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,180 control chromosomes in the GnomAD database, including 945 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 0.10 (945 hom., cov: 33)
• Consequence: LINC02743 NR_120444.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276
• Publications: 1 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_120444.1. 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
	LINC02743	NR_120444.1		n.121+10585C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02743	ENST00000526254.1	TSL:5	n.121+10585C>T		intron	N/A
	LINC02743	ENST00000762255.1		n.263+10585C>T		intron	N/A
	LINC02743	ENST00000762256.1		n.273+10585C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15655 AN: 152062 Hom.: 942 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0842

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0529

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.0872

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.103 AC: 15680 AN: 152180 Hom.: 945 Cov.: 33 AF XY: 0.102 AC XY: 7583 AN XY: 74396

African (AFR) AF: 0.125 AC: 5180 AN: 41498

American (AMR) AF: 0.100 AC: 1529 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0842 AC: 292 AN: 3468

East Asian (EAS) AF: 0.231 AC: 1196 AN: 5170

South Asian (SAS) AF: 0.134 AC: 644 AN: 4822

European-Finnish (FIN) AF: 0.0529 AC: 560 AN: 10592

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.0872 AC: 5932 AN: 68018

Other (OTH) AF: 0.108 AC: 229 AN: 2112

Alfa AF: 0.0948 Hom.: 2400

Bravo AF: 0.108

Asia WGS AF: 0.185 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.4
DANN	Benign	0.74
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs2723603; hg19: chr11-133669387;