rs678134

Positions:

• chr2-219715826-A-G
• chr2-219715826-A-T

Variant summary

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

The ENST00000606673.1(LINC02832):​n.119-21628A>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 0.558 in 152,090 control chromosomes in the GnomAD database, including 24,803 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 0.56 (24803 hom., cov: 33)
• Consequence: LINC02832 ENST00000606673.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120

Genes affected

LINC02832 (HGNC:54366): (long intergenic non-protein coding RNA 2832)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02832	ENST00000606673.1	n.119-21628A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84794 AN: 151970 Hom.: 24777 Cov.: 33

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.558 AC: 84877 AN: 152090 Hom.: 24803 Cov.: 33 AF XY: 0.550 AC XY: 40887 AN XY: 74334

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.538

Alfa AF: 0.524 Hom.: 43131

Bravo AF: 0.565

Asia WGS AF: 0.394 AC: 1370 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs678134; hg19: chr2-220580548;