17-48643203-C-T

Variant names:

• chr17-48643203-C-T
• rs2326017
• NR_189645.1:n.577C>T

Variant summary

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

The NR_189645.1(LINC02086):​n.577C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 152,048 control chromosomes in the GnomAD database, including 11,919 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 0.38 (11919 hom., cov: 32)
• Consequence: LINC02086 NR_189645.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.610

Genes affected

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

LINC03057 (HGNC:56359): (long intergenic non-protein coding RNA 3057)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02086	NR_189645.1	n.577C>T		non_coding_transcript_exon_variant	Exon 1 of 8
LINC03057	NR_186590.1	n.248+3402G>A		intron_variant	Intron 1 of 1
LINC02086	NR_189644.1	n.452+125C>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03057	ENST00000433510.2	n.419+3402G>A		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57635 AN: 151930 Hom.: 11901 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.380 AC: 57705 AN: 152048 Hom.: 11919 Cov.: 32 AF XY: 0.383 AC XY: 28451 AN XY: 74300

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.353

Alfa AF: 0.300 Hom.: 16209

Bravo AF: 0.378

Asia WGS AF: 0.338 AC: 1174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.038
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: rs2326017; hg19: chr17-46720565;