rs2169288

Variant names:

• chr12-74388897-A-C
• rs2169288
• ENST00000551726.2:n.192+13107T>G

Your query was ambiguous. Multiple possible variants found:

• chr12-74388897-A-C
• chr12-74388897-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000551726.2(LINC02882):​n.192+13107T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.794 in 151,968 control chromosomes in the GnomAD database, including 50,359 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 0.79 (50359 hom., cov: 30)
• Consequence: LINC02882 ENST00000551726.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 = 0.917 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	ENST00000551726.2	n.192+13107T>G		intron_variant	Intron 2 of 6	4
LINC02882	ENST00000653134.1	n.234+13107T>G		intron_variant	Intron 2 of 8
LINC02882	ENST00000656876.1	n.235-11265T>G		intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes AF: 0.794 AC: 120635 AN: 151850 Hom.: 50341 Cov.: 30

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.961

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.937

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.914

Gnomad OTH AF: 0.809

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

GnomAD4 genome AF: 0.794 AC: 120699 AN: 151968 Hom.: 50359 Cov.: 30 AF XY: 0.800 AC XY: 59425 AN XY: 74278

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.939

Gnomad4 SAS AF: 0.937

Gnomad4 FIN AF: 0.968

Gnomad4 NFE AF: 0.914

Gnomad4 OTH AF: 0.811

Alfa AF: 0.817 Hom.: 5280

Bravo AF: 0.765

Asia WGS AF: 0.907 AC: 3155 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	1.1
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2169288; hg19: chr12-74782677;