11-112585498-T-C

Position:

• chr11-112585498-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000665326.1(LINC02763):​n.381-38316T>C variant causes a intron, non coding transcript 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 ENST00000665326.1 intron, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02763	ENST00000665326.1	n.381-38316T>C		intron_variant, non_coding_transcript_variant
LINC02763	ENST00000529238.5	n.478-36189T>C		intron_variant, non_coding_transcript_variant		3
LINC02763	ENST00000700968.1	n.242-38316T>C		intron_variant, non_coding_transcript_variant

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;