2-219715563-T-C

Variant names:

• chr2-219715563-T-C
• rs2385573
• ENST00000606673.1:n.119-21891T>C

Variant summary

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

The ENST00000606673.1(LINC02832):​n.119-21891T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,180 control chromosomes in the GnomAD database, including 4,439 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 0.23 (4439 hom., cov: 33)
• Consequence: LINC02832 ENST00000606673.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.949
• Publications: 1 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=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000606673.1. 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
	LINC02832	ENST00000606673.1	TSL:3	n.119-21891T>C		intron	N/A
	LINC02832	ENST00000724275.1		n.100-21891T>C		intron	N/A
	LINC02832	ENST00000724276.1		n.148+151T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35521 AN: 152062 Hom.: 4440 Cov.: 33

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.233 AC: 35524 AN: 152180 Hom.: 4439 Cov.: 33 AF XY: 0.232 AC XY: 17243 AN XY: 74400

African (AFR) AF: 0.165 AC: 6848 AN: 41510

American (AMR) AF: 0.225 AC: 3448 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 992 AN: 3468

East Asian (EAS) AF: 0.196 AC: 1014 AN: 5186

South Asian (SAS) AF: 0.217 AC: 1043 AN: 4814

European-Finnish (FIN) AF: 0.221 AC: 2341 AN: 10598

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19096 AN: 67986

Other (OTH) AF: 0.246 AC: 521 AN: 2116

Alfa AF: 0.251 Hom.: 811

Bravo AF: 0.229

Asia WGS AF: 0.199 AC: 690 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	14
DANN	Benign	0.56
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs2385573; hg19: chr2-220580285;