6-24721439-A-T

Variant names:

• chr6-24721439-A-T
• rs1923187
• ENST00000665572.2:n.-219A>T

Variant summary

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

The ENST00000665572.2(LINC02828):​n.-219A>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,214 control chromosomes in the GnomAD database, including 2,578 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 0.18 (2578 hom., cov: 33)
• Consequence: LINC02828 ENST00000665572.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470
• Publications: 3 publications found

Genes affected

LINC02828 (HGNC:54359): (long intergenic non-protein coding RNA 2828)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665572.2. 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
	LINC02828	ENST00000665572.2		n.-219A>T		upstream_gene	N/A
	LINC02828	ENST00000668439.1		n.-249A>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27134 AN: 152096 Hom.: 2576 Cov.: 33

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.0119

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.178 AC: 27158 AN: 152214 Hom.: 2578 Cov.: 33 AF XY: 0.178 AC XY: 13242 AN XY: 74416

African (AFR) AF: 0.144 AC: 5963 AN: 41534

American (AMR) AF: 0.148 AC: 2270 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 648 AN: 3472

East Asian (EAS) AF: 0.0119 AC: 62 AN: 5190

South Asian (SAS) AF: 0.106 AC: 513 AN: 4826

European-Finnish (FIN) AF: 0.246 AC: 2596 AN: 10574

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14416 AN: 67994

Other (OTH) AF: 0.173 AC: 366 AN: 2116

Alfa AF: 0.126 Hom.: 220

Bravo AF: 0.171

Asia WGS AF: 0.0620 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	5.2
DANN	Benign	0.91
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs1923187; hg19: chr6-24721667;