chr11-110392019-G-T

Variant names:

• chr11-110392019-G-T
• rs10891096
• ENST00000526605.6:n.564-14225G>T

Variant summary

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

The ENST00000526605.6(LINC02732):​n.564-14225G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0853 in 152,196 control chromosomes in the GnomAD database, including 995 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 0.085 (995 hom., cov: 32)
• Consequence: LINC02732 ENST00000526605.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 2 publications found

Genes affected

LINC02732 (HGNC:54249): (long intergenic non-protein coding RNA 2732)

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 (EAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000526605.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02732	NR_135100.2		n.675+9998G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02732	ENST00000526605.6	TSL:2	n.564-14225G>T		intron	N/A
	LINC02732	ENST00000655432.1		n.177-14225G>T		intron	N/A
	LINC02732	ENST00000655839.2		n.338+9998G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0853 AC: 12970 AN: 152078 Hom.: 989 Cov.: 32

Gnomad AFR AF: 0.0352

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.0596

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0531

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0685

Gnomad OTH AF: 0.0850

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

GnomAD4 genome AF: 0.0853 AC: 12986 AN: 152196 Hom.: 995 Cov.: 32 AF XY: 0.0891 AC XY: 6635 AN XY: 74432

African (AFR) AF: 0.0352 AC: 1461 AN: 41544

American (AMR) AF: 0.213 AC: 3259 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0596 AC: 207 AN: 3472

East Asian (EAS) AF: 0.338 AC: 1747 AN: 5176

South Asian (SAS) AF: 0.173 AC: 832 AN: 4812

European-Finnish (FIN) AF: 0.0531 AC: 562 AN: 10590

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0685 AC: 4659 AN: 68004

Other (OTH) AF: 0.0836 AC: 177 AN: 2116

Alfa AF: 0.0658 Hom.: 208

Bravo AF: 0.0980

Asia WGS AF: 0.200 AC: 696 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	3.6
DANN	Benign	0.67
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10891096; hg19: chr11-110262743;