17-48680213-G-T

Position:

• chr17-48680213-G-T

Variant summary

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

The ENST00000575202.3(LINC02086):​n.176-3026G>T 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 0.437 in 152,038 control chromosomes in the GnomAD database, including 16,444 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 0.44 (16444 hom., cov: 32)
• Consequence: LINC02086 ENST00000575202.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.692

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02086	ENST00000575202.3	n.176-3026G>T		intron_variant, non_coding_transcript_variant		5
LINC02086	ENST00000628006.2	n.182-3026G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66316 AN: 151920 Hom.: 16400 Cov.: 32

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.437 AC: 66411 AN: 152038 Hom.: 16444 Cov.: 32 AF XY: 0.437 AC XY: 32489 AN XY: 74312

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.397

Alfa AF: 0.332 Hom.: 9581

Bravo AF: 0.444

Asia WGS AF: 0.382 AC: 1331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.28
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3096644; hg19: chr17-46757575;