rs7117858

Variant names:

• chr11-15672916-G-A
• rs7117858
• ENST00000532242.2:n.365+28881G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-15672916-G-A
• chr11-15672916-G-C

Variant summary

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

The ENST00000532242.2(LINC02751):​n.365+28881G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 152,018 control chromosomes in the GnomAD database, including 43,201 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 0.75 (43201 hom., cov: 32)
• Consequence: LINC02751 ENST00000532242.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 36 publications found

Genes affected

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

ENSG00000295141 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02751	NR_169502.1	n.756+28881G>A		intron_variant	Intron 4 of 5
LINC02751	NR_169503.1	n.770+28881G>A		intron_variant	Intron 4 of 5
LINC02751	NR_169507.1	n.84-31417G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02751	ENST00000532242.2	n.365+28881G>A		intron_variant	Intron 2 of 3	3
LINC02751	ENST00000717917.1	n.768-31422G>A		intron_variant	Intron 2 of 3
LINC02751	ENST00000717918.1	n.767-31417G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114245 AN: 151900 Hom.: 43166 Cov.: 32

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.752 AC: 114333 AN: 152018 Hom.: 43201 Cov.: 32 AF XY: 0.749 AC XY: 55652 AN XY: 74304

African (AFR) AF: 0.706 AC: 29309 AN: 41492

American (AMR) AF: 0.774 AC: 11814 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2444 AN: 3470

East Asian (EAS) AF: 0.787 AC: 4048 AN: 5146

South Asian (SAS) AF: 0.836 AC: 4026 AN: 4818

European-Finnish (FIN) AF: 0.642 AC: 6777 AN: 10550

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.787 AC: 53487 AN: 67966

Other (OTH) AF: 0.755 AC: 1594 AN: 2110

Alfa AF: 0.774 Hom.: 142309

Bravo AF: 0.754

Asia WGS AF: 0.791 AC: 2749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.76
DANN	Benign	0.33
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs7117858; hg19: chr11-15694462;