rs9319866

Positions:

• chr18-73247779-G-A

Variant summary

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

The NR_034133.1(LINC02864):​n.365+8034C>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 0.109 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 NR_034133.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.997

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02864	NR_034133.1	n.365+8034C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02864	ENST00000584544.5	n.170+8034C>T		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.0839

Gnomad4 EAS AF: 0.0356

Gnomad4 SAS AF: 0.0899

Gnomad4 FIN AF: 0.0342

Gnomad4 NFE AF: 0.0520

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0679 Hom.: 682

Bravo AF: 0.126

Asia WGS AF: 0.0680 AC: 238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9319866; hg19: chr18-70915014;