rs9963861

Variant names:

• chr18-73151908-A-G
• rs9963861
• ENST00000584544.5:n.1115-386T>C

Variant summary

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

The ENST00000584544.5(LINC02864):​n.1115-386T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,146 control chromosomes in the GnomAD database, including 2,767 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 (2767 hom., cov: 32)
• Consequence: LINC02864 ENST00000584544.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.346
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02864	ENST00000584544.5	n.1115-386T>C		intron_variant	Intron 9 of 9	1
LINC02864	ENST00000850060.1	n.840-386T>C		intron_variant	Intron 6 of 6
LINC02864	ENST00000850061.1	n.984-386T>C		intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16446 AN: 152028 Hom.: 2758 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0467

Gnomad ASJ AF: 0.00606

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00497

Gnomad FIN AF: 0.000753

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.00776

Gnomad OTH AF: 0.0932

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

GnomAD4 genome AF: 0.108 AC: 16496 AN: 152146 Hom.: 2767 Cov.: 32 AF XY: 0.105 AC XY: 7812 AN XY: 74404

African (AFR) AF: 0.362 AC: 14988 AN: 41434

American (AMR) AF: 0.0465 AC: 711 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00606 AC: 21 AN: 3464

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5174

South Asian (SAS) AF: 0.00518 AC: 25 AN: 4826

European-Finnish (FIN) AF: 0.000753 AC: 8 AN: 10622

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.00775 AC: 527 AN: 68020

Other (OTH) AF: 0.0922 AC: 195 AN: 2114

Alfa AF: 0.0790 Hom.: 265

Bravo AF: 0.125

Asia WGS AF: 0.0240 AC: 84 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.43
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs9963861; hg19: chr18-70819143;