11-15688538-T-G

Variant names:

• chr11-15688538-T-G
• rs7108738
• ENST00000532242.2:n.366-15795T>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000532242.2(LINC02751):​n.366-15795T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,098 control chromosomes in the GnomAD database, including 3,845 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 0.22 (3845 hom., cov: 32)
• Consequence: LINC02751 ENST00000532242.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.658
• Publications: 41 publications found

Genes affected

LINC02751 (HGNC:54271): (long intergenic non-protein coding RNA 2751)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000532242.2. 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
	LINC02751	NR_169502.1		n.757-15795T>G		intron	N/A
	LINC02751	NR_169503.1		n.771-15795T>G		intron	N/A
	LINC02751	NR_169507.1		n.84-15795T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02751	ENST00000532242.2	TSL:3	n.366-15795T>G		intron	N/A
	LINC02751	ENST00000717917.1		n.768-15800T>G		intron	N/A
	LINC02751	ENST00000717918.1		n.767-15795T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33222 AN: 151978 Hom.: 3839 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.219 AC: 33253 AN: 152098 Hom.: 3845 Cov.: 32 AF XY: 0.222 AC XY: 16505 AN XY: 74356

African (AFR) AF: 0.263 AC: 10929 AN: 41484

American (AMR) AF: 0.209 AC: 3199 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 926 AN: 3470

East Asian (EAS) AF: 0.184 AC: 948 AN: 5166

South Asian (SAS) AF: 0.127 AC: 613 AN: 4822

European-Finnish (FIN) AF: 0.340 AC: 3595 AN: 10562

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12276 AN: 67982

Other (OTH) AF: 0.224 AC: 474 AN: 2114

Alfa AF: 0.193 Hom.: 9538

Bravo AF: 0.217

Asia WGS AF: 0.181 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	14
DANN	Benign	0.79
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs7108738; hg19: chr11-15710084;