rs1919008

Positions:

• chr3-107110485-A-C
• chr3-107110485-A-T

Variant summary

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

The NR_028303.1(LINC00882):​n.389-481T>G 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 0.839 in 152,162 control chromosomes in the GnomAD database, including 53,981 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 0.84 (53980 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: LINC00882 NR_028303.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

Genes affected

LINC00882 (HGNC:48568): (long intergenic non-protein coding RNA 882)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00882	NR_028303.1	n.389-481T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00882	ENST00000660862.1	n.326+19403T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.839 AC: 127635 AN: 152044 Hom.: 53955 Cov.: 32

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.946

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.868

Gnomad OTH AF: 0.834

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.839 AC: 127694 AN: 152160 Hom.: 53980 Cov.: 32 AF XY: 0.843 AC XY: 62676 AN XY: 74380

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.945

Gnomad4 FIN AF: 0.909

Gnomad4 NFE AF: 0.868

Gnomad4 OTH AF: 0.837

Alfa AF: 0.844 Hom.: 5703

Bravo AF: 0.831

Asia WGS AF: 0.951 AC: 3304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1919008; hg19: chr3-106829332;