chr17-48643203-C-T

Variant names:

• chr17-48643203-C-T
• rs2326017
• ENST00000765378.1:n.577C>T

Variant summary

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

The ENST00000765378.1(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 ENST00000765378.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.610
• Publications: 24 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765378.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02086	NR_189645.1		n.577C>T		non_coding_transcript_exon	Exon 1 of 8
	LINC03057	NR_186590.1		n.248+3402G>A		intron	N/A
	LINC02086	NR_189644.1		n.452+125C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02086	ENST00000765378.1		n.577C>T		non_coding_transcript_exon	Exon 1 of 1
	LINC03057	ENST00000433510.3	TSL:2	n.446+3402G>A		intron	N/A
	LINC02086	ENST00000765377.1		n.270+125C>T		intron	N/A

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

African (AFR) AF: 0.554 AC: 22956 AN: 41466

American (AMR) AF: 0.301 AC: 4601 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1117 AN: 3466

East Asian (EAS) AF: 0.413 AC: 2140 AN: 5180

South Asian (SAS) AF: 0.279 AC: 1347 AN: 4822

European-Finnish (FIN) AF: 0.436 AC: 4594 AN: 10544

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19851 AN: 67978

Other (OTH) AF: 0.353 AC: 743 AN: 2106

Alfa AF: 0.316 Hom.: 28589

Bravo AF: 0.378

Asia WGS AF: 0.338 AC: 1174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.038
DANN	Benign	0.76
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs2326017; hg19: chr17-46720565;