ENST00000513853.6:n.220+8061G>A

Variant names:

• chr11-28710895-G-A
• rs1879445
• ENST00000513853.6:n.220+8061G>A

Variant summary

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

The ENST00000513853.6(LINC02742):​n.220+8061G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 151,806 control chromosomes in the GnomAD database, including 30,585 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 0.63 (30585 hom., cov: 30)
• Consequence: LINC02742 ENST00000513853.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 4 publications found

Genes affected

LINC02742 (HGNC:54259): (long intergenic non-protein coding RNA 2742)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513853.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02742	ENST00000513853.6	TSL:3	n.220+8061G>A		intron	N/A
	LINC02742	ENST00000662190.1		n.228+8061G>A		intron	N/A
	LINC02742	ENST00000788052.1		n.210+8061G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95156 AN: 151688 Hom.: 30564 Cov.: 30

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.627 AC: 95230 AN: 151806 Hom.: 30585 Cov.: 30 AF XY: 0.631 AC XY: 46795 AN XY: 74188

African (AFR) AF: 0.504 AC: 20828 AN: 41360

American (AMR) AF: 0.685 AC: 10454 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2223 AN: 3468

East Asian (EAS) AF: 0.903 AC: 4635 AN: 5134

South Asian (SAS) AF: 0.489 AC: 2347 AN: 4804

European-Finnish (FIN) AF: 0.772 AC: 8135 AN: 10532

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.653 AC: 44392 AN: 67938

Other (OTH) AF: 0.638 AC: 1346 AN: 2110

Alfa AF: 0.647 Hom.: 57216

Bravo AF: 0.623

Asia WGS AF: 0.700 AC: 2437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.63
PhyloP100		0.044

Splicing

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

Other links and lift over

dbSNP: rs1879445; hg19: chr11-28732442;