3-184749782-C-T

Variant names:

• chr3-184749782-C-T
• rs727272
• ENST00000657359.1:n.496+8725G>A

Variant summary

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

The ENST00000657359.1(LINC02069):​n.496+8725G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0937 in 152,154 control chromosomes in the GnomAD database, including 1,601 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 0.094 (1601 hom., cov: 32)
• Consequence: LINC02069 ENST00000657359.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480
• Publications: 4 publications found

Genes affected

LINC02069 (HGNC:52915): (long intergenic non-protein coding RNA 2069)

ENSG00000272970 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657359.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02069	ENST00000657359.1		n.496+8725G>A		intron	N/A
	ENSG00000272970	ENST00000716395.1		n.343-26194C>T		intron	N/A
	ENSG00000272970	ENST00000716398.1		n.629-9838C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0934 AC: 14204 AN: 152038 Hom.: 1593 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0455

Gnomad ASJ AF: 0.0369

Gnomad EAS AF: 0.00923

Gnomad SAS AF: 0.0505

Gnomad FIN AF: 0.00811

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0227

Gnomad OTH AF: 0.0707

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

GnomAD4 genome AF: 0.0937 AC: 14255 AN: 152154 Hom.: 1601 Cov.: 32 AF XY: 0.0897 AC XY: 6674 AN XY: 74384

African (AFR) AF: 0.274 AC: 11342 AN: 41468

American (AMR) AF: 0.0456 AC: 697 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0369 AC: 128 AN: 3468

East Asian (EAS) AF: 0.00926 AC: 48 AN: 5186

South Asian (SAS) AF: 0.0497 AC: 239 AN: 4810

European-Finnish (FIN) AF: 0.00811 AC: 86 AN: 10608

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0227 AC: 1544 AN: 68002

Other (OTH) AF: 0.0723 AC: 153 AN: 2116

Alfa AF: 0.0536 Hom.: 389

Bravo AF: 0.104

Asia WGS AF: 0.0630 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.51
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs727272; hg19: chr3-184467570;