rs2286983

Positions:

• chr3-172574694-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_146714.1(LINC02068):​n.327-354C>T 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 0.288 in 152,138 control chromosomes in the GnomAD database, including 6,853 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 0.29 (6853 hom., cov: 32)
• Consequence: LINC02068 NR_146714.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

Genes affected

LINC02068 (HGNC:52914): (long intergenic non-protein coding RNA 2068)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02068	NR_146714.1	n.327-354C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02068	ENST00000424941.2	n.327-354C>T		intron_variant, non_coding_transcript_variant		2
LINC02068	ENST00000441185.6	n.147-13625C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43788 AN: 152020 Hom.: 6826 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.288 AC: 43868 AN: 152138 Hom.: 6853 Cov.: 32 AF XY: 0.289 AC XY: 21472 AN XY: 74376

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.258

Alfa AF: 0.235 Hom.: 9001

Bravo AF: 0.292

Asia WGS AF: 0.312 AC: 1082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2286983; hg19: chr3-172292484;