rs2165207

Variant names:

• chr12-73738488-A-C
• rs2165207
• ENST00000716241.1:n.259+82322T>G

Your query was ambiguous. Multiple possible variants found:

• chr12-73738488-A-C
• chr12-73738488-A-G

Variant summary

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

The ENST00000716241.1(LINC02882):​n.259+82322T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 151,434 control chromosomes in the GnomAD database, including 13,819 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 0.41 (13819 hom., cov: 30)
• Consequence: LINC02882 ENST00000716241.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 1 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716241.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02882	ENST00000716241.1		n.259+82322T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62054 AN: 151316 Hom.: 13803 Cov.: 30

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.410 AC: 62109 AN: 151434 Hom.: 13819 Cov.: 30 AF XY: 0.404 AC XY: 29867 AN XY: 73924

African (AFR) AF: 0.581 AC: 23932 AN: 41188

American (AMR) AF: 0.329 AC: 5018 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1204 AN: 3466

East Asian (EAS) AF: 0.155 AC: 797 AN: 5150

South Asian (SAS) AF: 0.282 AC: 1360 AN: 4822

European-Finnish (FIN) AF: 0.370 AC: 3832 AN: 10364

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.363 AC: 24655 AN: 67904

Other (OTH) AF: 0.372 AC: 784 AN: 2108

Alfa AF: 0.220 Hom.: 450

Bravo AF: 0.419

Asia WGS AF: 0.235 AC: 819 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	0.57
DANN	Benign	0.56
PhyloP100		-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2165207;

hg19: chr12-74132268;