rs727272

chr3-184749782-C-T

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02069	ENST00000657359.1	n.496+8725G>A		intron_variant, non_coding_transcript_variant

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;