rs9319866

Variant names:

• chr18-73247779-G-A
• rs9319866
• ENST00000581011.5:n.347+8034C>T

Variant summary

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

The ENST00000581011.5(LINC02864):​n.347+8034C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,080 control chromosomes in the GnomAD database, including 1,402 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 0.11 (1402 hom., cov: 33)
• Consequence: LINC02864 ENST00000581011.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.997
• Publications: 5 publications found

Genes affected

LINC02864 (HGNC:54480): (long intergenic non-protein coding RNA 2864)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000581011.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02864	NR_034133.1		n.365+8034C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02864	ENST00000581011.5	TSL:1	n.347+8034C>T		intron	N/A
	LINC02864	ENST00000581862.7	TSL:1	n.400+8034C>T		intron	N/A
	LINC02864	ENST00000584544.5	TSL:1	n.170+8034C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16598 AN: 151962 Hom.: 1395 Cov.: 33

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.0839

Gnomad EAS AF: 0.0355

Gnomad SAS AF: 0.0900

Gnomad FIN AF: 0.0342

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0520

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.109 AC: 16642 AN: 152080 Hom.: 1402 Cov.: 33 AF XY: 0.111 AC XY: 8253 AN XY: 74336

African (AFR) AF: 0.205 AC: 8484 AN: 41464

American (AMR) AF: 0.201 AC: 3074 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0839 AC: 291 AN: 3470

East Asian (EAS) AF: 0.0356 AC: 184 AN: 5164

South Asian (SAS) AF: 0.0899 AC: 432 AN: 4808

European-Finnish (FIN) AF: 0.0342 AC: 362 AN: 10590

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0520 AC: 3534 AN: 67990

Other (OTH) AF: 0.108 AC: 228 AN: 2110

Alfa AF: 0.0752 Hom.: 1120

Bravo AF: 0.126

Asia WGS AF: 0.0680 AC: 238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.54
PhyloP100		1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9319866;

hg19: chr18-70915014;