ENST00000427290.2:n.254+36387C>T

Variant names:

• chr1-112323975-G-A
• rs11102457
• ENST00000427290.2:n.254+36387C>T

Variant summary

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

The ENST00000427290.2(LINC02884):​n.254+36387C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,200 control chromosomes in the GnomAD database, including 1,858 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 0.15 (1858 hom., cov: 33)
• Consequence: LINC02884 ENST00000427290.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.403
• Publications: 1 publications found

Genes affected

LINC02884 (HGNC:54808): (long intergenic non-protein coding RNA 2884)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02884	NR_183465.1	n.246+36387C>T		intron_variant	Intron 1 of 2
LINC02884	NR_183466.1	n.246+36387C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02884	ENST00000427290.2	n.254+36387C>T		intron_variant	Intron 1 of 1	3
LINC02884	ENST00000654472.1	n.145+36387C>T		intron_variant	Intron 1 of 2
LINC02884	ENST00000658120.2	n.352+36387C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23568 AN: 152082 Hom.: 1858 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.155 AC: 23582 AN: 152200 Hom.: 1858 Cov.: 33 AF XY: 0.155 AC XY: 11557 AN XY: 74414

African (AFR) AF: 0.161 AC: 6680 AN: 41544

American (AMR) AF: 0.114 AC: 1737 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 543 AN: 3472

East Asian (EAS) AF: 0.245 AC: 1269 AN: 5170

South Asian (SAS) AF: 0.202 AC: 975 AN: 4822

European-Finnish (FIN) AF: 0.163 AC: 1722 AN: 10594

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10180 AN: 67994

Other (OTH) AF: 0.133 AC: 281 AN: 2110

Alfa AF: 0.149 Hom.: 3356

Bravo AF: 0.148

Asia WGS AF: 0.204 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.0
DANN	Benign	0.42
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs11102457; hg19: chr1-112866597;