rs2564866

Variant names:

• chr11-112276936-A-G
• rs2564866
• ENST00000729087.1:n.369A>G

Variant summary

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

The ENST00000729087.1(LINC02762):​n.369A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.73 in 151,356 control chromosomes in the GnomAD database, including 40,374 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 0.73 (40374 hom., cov: 30)
• Consequence: LINC02762 ENST00000729087.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.22
• Publications: 3 publications found

Genes affected

LINC02762 (HGNC:27443): (long intergenic non-protein coding RNA 2762)

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 (SAS) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729087.1. 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
	LINC02762	NR_126004.1		n.35+6153A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02762	ENST00000729087.1		n.369A>G		non_coding_transcript_exon	Exon 2 of 2
	LINC02762	ENST00000504610.2	TSL:2	n.35+6153A>G		intron	N/A
	LINC02762	ENST00000532168.4	TSL:3	n.78-3548A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110307 AN: 151238 Hom.: 40317 Cov.: 30

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.730 AC: 110426 AN: 151356 Hom.: 40374 Cov.: 30 AF XY: 0.729 AC XY: 53857 AN XY: 73910

African (AFR) AF: 0.692 AC: 28498 AN: 41200

American (AMR) AF: 0.770 AC: 11720 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 2719 AN: 3464

East Asian (EAS) AF: 0.786 AC: 4034 AN: 5132

South Asian (SAS) AF: 0.799 AC: 3833 AN: 4796

European-Finnish (FIN) AF: 0.706 AC: 7380 AN: 10460

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.735 AC: 49787 AN: 67776

Other (OTH) AF: 0.737 AC: 1550 AN: 2102

Alfa AF: 0.734 Hom.: 11886

Bravo AF: 0.733

Asia WGS AF: 0.772 AC: 2685 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	0.014
DANN	Benign	0.33
PhyloP100		-3.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2564866;

hg19: chr11-112147659;