3-107117393-C-T

Variant summary

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

The NR_028303.1(LINC00882):n.302-5247G>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 0.254 in 152,054 control chromosomes in the GnomAD database, including 5,308 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 0.25 (5308 hom., cov: 31)
• Consequence: LINC00882 NR_028303.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00882	NR_028303.1	n.302-5247G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00882	ENST00000660862.1	n.326+12495G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38511 AN: 151936 Hom.: 5287 Cov.: 31

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.254 AC: 38586 AN: 152054 Hom.: 5308 Cov.: 31 AF XY: 0.250 AC XY: 18609 AN XY: 74320

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.241

Alfa AF: 0.219 Hom.: 5251

Bravo AF: 0.259

Asia WGS AF: 0.214 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.51
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9863794; hg19: chr3-106836240;