12-74258017-T-G

Variant names:

• chr12-74258017-T-G
• rs7294453
• ENST00000515416.8:n.783+27008A>C

Variant summary

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

The ENST00000515416.8(LINC02882):​n.783+27008A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.091 in 152,142 control chromosomes in the GnomAD database, including 737 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 0.091 (737 hom., cov: 32)
• Consequence: LINC02882 ENST00000515416.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02882	NR_038300.1	n.473+27008A>C		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02882	ENST00000515416.8	n.783+27008A>C		intron_variant	Intron 3 of 3	1
LINC02882	ENST00000549905.5	n.473+27008A>C		intron_variant	Intron 3 of 6	1
LINC02882	ENST00000551726.2	n.620+27008A>C		intron_variant	Intron 6 of 6	4

Frequencies

GnomAD3 genomes AF: 0.0911 AC: 13844 AN: 152024 Hom.: 740 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0614

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.0129

Gnomad SAS AF: 0.0733

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.0734

Gnomad OTH AF: 0.0831

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

GnomAD4 genome AF: 0.0910 AC: 13846 AN: 152142 Hom.: 737 Cov.: 32 AF XY: 0.0899 AC XY: 6683 AN XY: 74366

African (AFR) AF: 0.153 AC: 6348 AN: 41538

American (AMR) AF: 0.0613 AC: 937 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0945 AC: 328 AN: 3470

East Asian (EAS) AF: 0.0129 AC: 67 AN: 5182

South Asian (SAS) AF: 0.0721 AC: 348 AN: 4824

European-Finnish (FIN) AF: 0.0532 AC: 564 AN: 10594

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.0734 AC: 4987 AN: 67934

Other (OTH) AF: 0.0822 AC: 174 AN: 2116

Alfa AF: 0.0711 Hom.: 277

Bravo AF: 0.0941

Asia WGS AF: 0.0430 AC: 150 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.0
DANN	Benign	0.66
PhyloP100		0.18
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7294453; hg19: chr12-74651797;