11-112585739-A-G

Variant names:

• chr11-112585739-A-G
• rs7108821
• ENST00000529238.5:n.478-35948A>G

Variant summary

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

The ENST00000529238.5(LINC02763):​n.478-35948A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 151,940 control chromosomes in the GnomAD database, including 29,676 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 0.62 (29676 hom., cov: 31)
• Consequence: LINC02763 ENST00000529238.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870
• Publications: 6 publications found

Genes affected

LINC02763 (HGNC:54282): (long intergenic non-protein coding RNA 2763)

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 = 0.763 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000529238.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02763	ENST00000529238.5	TSL:3	n.478-35948A>G		intron	N/A
	LINC02763	ENST00000665326.1		n.381-38075A>G		intron	N/A
	LINC02763	ENST00000700968.1		n.242-38075A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94704 AN: 151822 Hom.: 29657 Cov.: 31

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.624 AC: 94780 AN: 151940 Hom.: 29676 Cov.: 31 AF XY: 0.630 AC XY: 46813 AN XY: 74260

African (AFR) AF: 0.579 AC: 23997 AN: 41434

American (AMR) AF: 0.704 AC: 10747 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2346 AN: 3464

East Asian (EAS) AF: 0.615 AC: 3172 AN: 5156

South Asian (SAS) AF: 0.784 AC: 3776 AN: 4818

European-Finnish (FIN) AF: 0.692 AC: 7306 AN: 10554

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41233 AN: 67950

Other (OTH) AF: 0.630 AC: 1325 AN: 2104

Alfa AF: 0.612 Hom.: 4774

Bravo AF: 0.620

Asia WGS AF: 0.713 AC: 2480 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	0.24
DANN	Benign	0.50
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs7108821; hg19: chr11-112456462;