11-112585498-T-C

Variant names:

• chr11-112585498-T-C
• rs7105881
• ENST00000529238.5:n.478-36189T>C

Variant summary

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

The ENST00000529238.5(LINC02763):​n.478-36189T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 152,024 control chromosomes in the GnomAD database, including 29,635 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 (29635 hom., cov: 31)
• Consequence: LINC02763 ENST00000529238.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183
• Publications: 15 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=-0.92).
• 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.478-36189T>C		intron	N/A
	LINC02763	ENST00000665326.1		n.381-38316T>C		intron	N/A
	LINC02763	ENST00000700968.1		n.242-38316T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94655 AN: 151906 Hom.: 29616 Cov.: 31

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.623 AC: 94731 AN: 152024 Hom.: 29635 Cov.: 31 AF XY: 0.630 AC XY: 46787 AN XY: 74284

African (AFR) AF: 0.579 AC: 23989 AN: 41438

American (AMR) AF: 0.704 AC: 10754 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2346 AN: 3470

East Asian (EAS) AF: 0.613 AC: 3158 AN: 5154

South Asian (SAS) AF: 0.784 AC: 3766 AN: 4804

European-Finnish (FIN) AF: 0.692 AC: 7326 AN: 10582

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41189 AN: 67978

Other (OTH) AF: 0.628 AC: 1326 AN: 2110

Alfa AF: 0.612 Hom.: 125514

Bravo AF: 0.620

Asia WGS AF: 0.713 AC: 2481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.4
DANN	Benign	0.61
PhyloP100		-0.18

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: rs7105881;

hg19: chr11-112456221;