12-74388897-A-C

Variant names:

• chr12-74388897-A-C
• rs2169288
• ENST00000548427.2:n.64-11265T>G

Variant summary

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

The ENST00000548427.2(LINC02882):​n.64-11265T>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 ENST00000548427.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• Publications: 2 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 = 0.917 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000548427.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02882	ENST00000548427.2	TSL:6	n.64-11265T>G		intron	N/A
	LINC02882	ENST00000551726.2	TSL:4	n.192+13107T>G		intron	N/A
	LINC02882	ENST00000653134.1		n.234+13107T>G		intron	N/A

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

African (AFR) AF: 0.512 AC: 21197 AN: 41414

American (AMR) AF: 0.772 AC: 11781 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3173 AN: 3470

East Asian (EAS) AF: 0.939 AC: 4821 AN: 5132

South Asian (SAS) AF: 0.937 AC: 4511 AN: 4814

European-Finnish (FIN) AF: 0.968 AC: 10229 AN: 10564

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.914 AC: 62148 AN: 68004

Other (OTH) AF: 0.811 AC: 1709 AN: 2108

Alfa AF: 0.801 Hom.: 5380

Bravo AF: 0.765

Asia WGS AF: 0.907 AC: 3155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.28
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs2169288; hg19: chr12-74782677;