3-107117393-C-T

Variant names:

• chr3-107117393-C-T
• rs9863794
• ENST00000484698.5:n.295+12495G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000484698.5(LINC00882):​n.295+12495G>A variant causes a intron 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 ENST00000484698.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000484698.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00882	NR_028303.1		n.302-5247G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00882	ENST00000484698.5	TSL:1	n.295+12495G>A		intron	N/A
	LINC00882	ENST00000473636.2	TSL:3	n.441-5247G>A		intron	N/A
	LINC00882	ENST00000477210.7	TSL:2	n.482-5247G>A		intron	N/A

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

African (AFR) AF: 0.363 AC: 15055 AN: 41438

American (AMR) AF: 0.197 AC: 3005 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 898 AN: 3470

East Asian (EAS) AF: 0.279 AC: 1439 AN: 5162

South Asian (SAS) AF: 0.122 AC: 586 AN: 4820

European-Finnish (FIN) AF: 0.218 AC: 2309 AN: 10576

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.211 AC: 14317 AN: 67990

Other (OTH) AF: 0.241 AC: 510 AN: 2112

Alfa AF: 0.222 Hom.: 6855

Bravo AF: 0.259

Asia WGS AF: 0.214 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.51
DANN	Benign	0.37
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs9863794; hg19: chr3-106836240;