rs2169288

chr12-74388897-A-Cchr12-74388897-A-T

Variant summary

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

The ENST00000663261.1(LINC02882):n.68-11265T>G variant causes a intron, non coding transcript 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 ENST00000663261.1 intron, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02882	ENST00000663261.1	n.68-11265T>G		intron_variant, non_coding_transcript_variant

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;