rs3802557

Positions:

• chr10-16283879-T-G

Variant summary

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

The NR_184075.1(LINC02654):​n.843T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,192 control chromosomes in the GnomAD database, including 31,228 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 0.61 (31145 hom., cov: 31)
  • Exomes 𝑓: 0.79 (83 hom.)
• Consequence: LINC02654 NR_184075.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818

Genes affected

LINC02654 (HGNC:54140): (long intergenic non-protein coding RNA 2654)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02654	NR_184075.1	n.843T>G		non_coding_transcript_exon_variant	2/4
LINC02654	NR_184073.1	n.843T>G		non_coding_transcript_exon_variant	2/3
LINC02654	NR_184074.1	n.693+5130T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02654	ENST00000652949.1	n.657+5130T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92365 AN: 151812 Hom.: 31141 Cov.: 31

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.633

GnomAD4 exome AF: 0.792 AC: 206 AN: 260 Hom.: 83 Cov.: 0 AF XY: 0.762 AC XY: 125 AN XY: 164

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.773

Gnomad4 NFE exome AF: 0.855

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.608 AC: 92390 AN: 151932 Hom.: 31145 Cov.: 31 AF XY: 0.611 AC XY: 45360 AN XY: 74276

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.746

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.632

Alfa AF: 0.726 Hom.: 59555

Bravo AF: 0.588

Asia WGS AF: 0.597 AC: 2077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.24
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3802557; hg19: chr10-16325878;