chr17-48703467-A-G

Variant names:

• chr17-48703467-A-G
• rs8064938
• ENST00000492522.3:n.137-534A>G

Variant summary

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

The ENST00000492522.3(LINC02086):​n.137-534A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 152,114 control chromosomes in the GnomAD database, including 45,095 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 0.76 (45095 hom., cov: 32)
• Consequence: LINC02086 ENST00000492522.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02086	NR_189644.1	n.761-534A>G		intron_variant	Intron 4 of 5
LINC02086	NR_189645.1	n.4176-534A>G		intron_variant	Intron 6 of 7
LINC02086	NR_189646.1	n.431-534A>G		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02086	ENST00000492522.3	n.137-534A>G		intron_variant	Intron 2 of 3	5
LINC02086	ENST00000575202.3	n.355-534A>G		intron_variant	Intron 4 of 4	5
LINC02086	ENST00000628006.2	n.575-534A>G		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115510 AN: 151998 Hom.: 45082 Cov.: 32

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.760 AC: 115566 AN: 152114 Hom.: 45095 Cov.: 32 AF XY: 0.754 AC XY: 56086 AN XY: 74356

African (AFR) AF: 0.681 AC: 28258 AN: 41474

American (AMR) AF: 0.715 AC: 10920 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2835 AN: 3472

East Asian (EAS) AF: 0.243 AC: 1257 AN: 5174

South Asian (SAS) AF: 0.682 AC: 3285 AN: 4818

European-Finnish (FIN) AF: 0.854 AC: 9037 AN: 10586

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.844 AC: 57402 AN: 68000

Other (OTH) AF: 0.753 AC: 1591 AN: 2114

Alfa AF: 0.812 Hom.: 94233

Bravo AF: 0.742

Asia WGS AF: 0.474 AC: 1652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.7
DANN	Benign	0.52
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs8064938; hg19: chr17-46780829;