2-219715826-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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
LINC02832	ENST00000724275.1	n.100-21628A>G		intron_variant	Intron 1 of 1
LINC02832	ENST00000724276.1	n.149-139A>G		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.715 AC: 29640 AN: 41482

American (AMR) AF: 0.486 AC: 7437 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2034 AN: 3468

East Asian (EAS) AF: 0.260 AC: 1348 AN: 5178

South Asian (SAS) AF: 0.413 AC: 1991 AN: 4820

European-Finnish (FIN) AF: 0.475 AC: 5017 AN: 10568

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35685 AN: 67968

Other (OTH) AF: 0.538 AC: 1136 AN: 2110

Alfa AF: 0.534 Hom.: 70264

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
PhyloP100		-0.012

Splicing

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

Other links and lift over

dbSNP: rs678134; hg19: chr2-220580548;