rs17112634

Variant names:

• chr12-73729522-G-A
• rs17112634
• ENST00000716241.1:n.259+91288C>T

Variant summary

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

The ENST00000716241.1(LINC02882):​n.259+91288C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0555 in 152,022 control chromosomes in the GnomAD database, including 248 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 0.055 (248 hom., cov: 32)
• Consequence: LINC02882 ENST00000716241.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0787 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+91288C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0556 AC: 8439 AN: 151904 Hom.: 248 Cov.: 32

Gnomad AFR AF: 0.0812

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0390

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.0100

Gnomad SAS AF: 0.0427

Gnomad FIN AF: 0.0463

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0482

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0555 AC: 8436 AN: 152022 Hom.: 248 Cov.: 32 AF XY: 0.0550 AC XY: 4089 AN XY: 74304

African (AFR) AF: 0.0810 AC: 3360 AN: 41472

American (AMR) AF: 0.0390 AC: 595 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0804 AC: 279 AN: 3472

East Asian (EAS) AF: 0.0100 AC: 52 AN: 5178

South Asian (SAS) AF: 0.0421 AC: 203 AN: 4824

European-Finnish (FIN) AF: 0.0463 AC: 490 AN: 10574

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0482 AC: 3276 AN: 67920

Other (OTH) AF: 0.0493 AC: 104 AN: 2110

Alfa AF: 0.0504 Hom.: 289

Bravo AF: 0.0554

Asia WGS AF: 0.0280 AC: 99 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.61
DANN	Benign	0.20
PhyloP100		-0.40

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: rs17112634;

hg19: chr12-74123302;