chr11-29008009-G-C

Variant names:

• chr11-29008009-G-C
• rs7928853
• ENST00000511073.2:n.124-29733G>C

Variant summary

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

The ENST00000511073.2(LINC02742):​n.124-29733G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.867 in 152,114 control chromosomes in the GnomAD database, including 58,329 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 0.87 (58329 hom., cov: 32)
• Consequence: LINC02742 ENST00000511073.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209
• Publications: 1 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=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000511073.2. 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
	LINC02742	NR_183752.1		n.134-29733G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02742	ENST00000511073.2	TSL:3	n.124-29733G>C		intron	N/A
	LINC02742	ENST00000513853.6	TSL:3	n.305-29733G>C		intron	N/A
	LINC02742	ENST00000788053.1		n.259-29733G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.867 AC: 131795 AN: 151994 Hom.: 58309 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.993

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.985

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.967

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.867 AC: 131859 AN: 152114 Hom.: 58329 Cov.: 32 AF XY: 0.867 AC XY: 64449 AN XY: 74364

African (AFR) AF: 0.684 AC: 28381 AN: 41472

American (AMR) AF: 0.843 AC: 12861 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.967 AC: 3357 AN: 3470

East Asian (EAS) AF: 0.784 AC: 4043 AN: 5158

South Asian (SAS) AF: 0.985 AC: 4752 AN: 4826

European-Finnish (FIN) AF: 0.906 AC: 9617 AN: 10614

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.967 AC: 65786 AN: 68010

Other (OTH) AF: 0.886 AC: 1870 AN: 2110

Alfa AF: 0.912 Hom.: 7939

Bravo AF: 0.853

Asia WGS AF: 0.893 AC: 3107 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	0.39
DANN	Benign	0.42
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs7928853; hg19: chr11-29029556;