rs8081391

Positions:

• chr17-48694838-G-A

Variant summary

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

The ENST00000575202.3(LINC02086):​n.355-9163G>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 0.162 in 152,060 control chromosomes in the GnomAD database, including 2,541 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 0.16 (2541 hom., cov: 31)
• Consequence: LINC02086 ENST00000575202.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.593

Genes affected

LINC02086 (HGNC:52936): (long intergenic non-protein coding RNA 2086)

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 = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02086	XR_934818.4	n.867-5774G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02086	ENST00000575202.3	n.355-9163G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24597 AN: 151942 Hom.: 2535 Cov.: 31

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.0864

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.0836

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.162 AC: 24633 AN: 152060 Hom.: 2541 Cov.: 31 AF XY: 0.165 AC XY: 12266 AN XY: 74346

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.0864

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.0836

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.175

Alfa AF: 0.141 Hom.: 3681

Bravo AF: 0.181

Asia WGS AF: 0.350 AC: 1212 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	8.6
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: rs8081391; hg19: chr17-46772200;