rs713279

Variant names:

• chr11-133693414-C-A
• rs713279
• ENST00000762255.1:n.378+31953G>T

Variant summary

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

The ENST00000762255.1(LINC02743):​n.378+31953G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,006 control chromosomes in the GnomAD database, including 4,230 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 0.22 (4230 hom., cov: 31)
• Consequence: LINC02743 ENST00000762255.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02743	ENST00000762255.1		n.378+31953G>T		intron	N/A
	LINC02743	ENST00000762256.1		n.388+31953G>T		intron	N/A
	LINC02743	ENST00000762257.1		n.402+31953G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32887 AN: 151888 Hom.: 4213 Cov.: 31

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.217 AC: 32926 AN: 152006 Hom.: 4230 Cov.: 31 AF XY: 0.225 AC XY: 16735 AN XY: 74306

African (AFR) AF: 0.157 AC: 6496 AN: 41482

American (AMR) AF: 0.413 AC: 6313 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 714 AN: 3468

East Asian (EAS) AF: 0.295 AC: 1517 AN: 5142

South Asian (SAS) AF: 0.421 AC: 2025 AN: 4812

European-Finnish (FIN) AF: 0.183 AC: 1936 AN: 10580

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13212 AN: 67938

Other (OTH) AF: 0.219 AC: 461 AN: 2104

Alfa AF: 0.208 Hom.: 12958

Bravo AF: 0.230

Asia WGS AF: 0.384 AC: 1336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.10
DANN	Benign	0.51
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs713279; hg19: chr11-133563309;