11-112585498-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02763	ENST00000529238.5	n.478-36189T>C		intron_variant	Intron 3 of 3	3
LINC02763	ENST00000665326.1	n.381-38316T>C		intron_variant	Intron 2 of 2
LINC02763	ENST00000700968.1	n.242-38316T>C		intron_variant	Intron 2 of 2

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

Gnomad4 AFR AF: 0.579

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.784

Gnomad4 FIN AF: 0.692

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.628

Alfa AF: 0.612 Hom.: 63943

Bravo AF: 0.620

Asia WGS AF: 0.713 AC: 2481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7105881; hg19: chr11-112456221;