12-73694028-C-T

Variant names:

• chr12-73694028-C-T
• rs7964120
• ENST00000716241.1:n.260-71058G>A

Variant summary

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

The ENST00000716241.1(LINC02882):​n.260-71058G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,946 control chromosomes in the GnomAD database, including 8,344 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 0.31 (8344 hom., cov: 32)
• Consequence: LINC02882 ENST00000716241.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160
• Publications: 7 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 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.260-71058G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46616 AN: 151828 Hom.: 8345 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.307 AC: 46622 AN: 151946 Hom.: 8344 Cov.: 32 AF XY: 0.312 AC XY: 23171 AN XY: 74264

African (AFR) AF: 0.140 AC: 5831 AN: 41504

American (AMR) AF: 0.328 AC: 4991 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1333 AN: 3470

East Asian (EAS) AF: 0.725 AC: 3752 AN: 5174

South Asian (SAS) AF: 0.377 AC: 1817 AN: 4824

European-Finnish (FIN) AF: 0.374 AC: 3941 AN: 10544

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23835 AN: 67886

Other (OTH) AF: 0.348 AC: 732 AN: 2102

Alfa AF: 0.338 Hom.: 29278

Bravo AF: 0.297

Asia WGS AF: 0.498 AC: 1730 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	1.3
DANN	Benign	0.64
PhyloP100		0.016

Splicing

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

Other links and lift over

dbSNP: rs7964120; hg19: chr12-74087808;