rs678134

Variant names:

• chr2-219715826-A-G
• rs678134
• ENST00000606673.1:n.119-21628A>G

Your query was ambiguous. Multiple possible variants found:

• 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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02832	ENST00000606673.1	n.119-21628A>G		intron_variant	Intron 1 of 1	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;