rs727272

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

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
LINC02069	ENST00000657359.1	n.496+8725G>A		intron_variant	Intron 3 of 3

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

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.0456

Gnomad4 ASJ AF: 0.0369

Gnomad4 EAS AF: 0.00926

Gnomad4 SAS AF: 0.0497

Gnomad4 FIN AF: 0.00811

Gnomad4 NFE AF: 0.0227

Gnomad4 OTH AF: 0.0723

Alfa AF: 0.0526 Hom.: 259

Bravo AF: 0.104

Asia WGS AF: 0.0630 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs727272; hg19: chr3-184467570;