chr3-82001133-A-G

Position:

• chr3-82001133-A-G

Variant summary

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

The ENST00000470263.5(LINC02008):​n.244+14752A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,210 control chromosomes in the GnomAD database, including 8,549 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 (8549 hom., cov: 33)
• Consequence: LINC02008 ENST00000470263.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

Genes affected

LINC02008 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02008	NR_147146.1	n.240+14752A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02008	ENST00000470263.5	n.244+14752A>G		intron_variant		1
LINC02008	ENST00000494340.2	n.230+14752A>G		intron_variant		2
LINC02008	ENST00000653255.1	n.206+14752A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43513 AN: 152092 Hom.: 8526 Cov.: 33

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.286 AC: 43579 AN: 152210 Hom.: 8549 Cov.: 33 AF XY: 0.277 AC XY: 20617 AN XY: 74418

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.260

Alfa AF: 0.200 Hom.: 6918

Bravo AF: 0.306

Asia WGS AF: 0.196 AC: 684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9875387; hg19: chr3-82050284;