ENST00000716241.1:n.260-96278T>C

Variant names:

• chr12-73719248-A-G
• rs7299914
• ENST00000716241.1:n.260-96278T>C

Variant summary

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

The ENST00000716241.1(LINC02882):​n.260-96278T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 151,760 control chromosomes in the GnomAD database, including 25,411 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 0.57 (25411 hom., cov: 31)
• Consequence: LINC02882 ENST00000716241.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787
• Publications: 4 publications found

Genes affected

LINC02882 (HGNC:54802): (long intergenic non-protein coding RNA 2882)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.755 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
LINC02882	ENST00000716241.1	n.260-96278T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87195 AN: 151644 Hom.: 25404 Cov.: 31

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.575 AC: 87237 AN: 151760 Hom.: 25411 Cov.: 31 AF XY: 0.577 AC XY: 42771 AN XY: 74176

African (AFR) AF: 0.516 AC: 21337 AN: 41370

American (AMR) AF: 0.538 AC: 8195 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1931 AN: 3470

East Asian (EAS) AF: 0.776 AC: 3963 AN: 5110

South Asian (SAS) AF: 0.603 AC: 2908 AN: 4820

European-Finnish (FIN) AF: 0.619 AC: 6528 AN: 10542

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40371 AN: 67896

Other (OTH) AF: 0.598 AC: 1258 AN: 2104

Alfa AF: 0.583 Hom.: 82179

Bravo AF: 0.565

Asia WGS AF: 0.648 AC: 2250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.26
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs7299914; hg19: chr12-74113028;