rs12072775

Variant names:

• chr1-229136806-C-A
• rs12072775
• ENST00000662083.1:n.47-43518G>T

Variant summary

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

The ENST00000662083.1(LINC02814):​n.47-43518G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0754 in 152,206 control chromosomes in the GnomAD database, including 512 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 0.075 (512 hom., cov: 32)
• Consequence: LINC02814 ENST00000662083.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338
• Publications: 2 publications found

Genes affected

LINC02814 (HGNC:54346): (long intergenic non-protein coding RNA 2814)

LINC02815 (HGNC:54347): (long intergenic non-protein coding RNA 2815)

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 = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02815	NR_186725.1	n.156+17764G>T		intron_variant	Intron 1 of 3
LINC02815	NR_186726.1	n.156+17764G>T		intron_variant	Intron 1 of 2
LINC02815	NR_186727.1	n.157-13693G>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02814	ENST00000662083.1	n.47-43518G>T		intron_variant	Intron 1 of 4
LINC02814	ENST00000666388.1	n.338-43518G>T		intron_variant	Intron 2 of 2
LINC02814	ENST00000716797.1	n.184-43518G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0754 AC: 11466 AN: 152086 Hom.: 510 Cov.: 32

Gnomad AFR AF: 0.0647

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0410

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0607

Gnomad OTH AF: 0.0759

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

GnomAD4 genome AF: 0.0754 AC: 11473 AN: 152206 Hom.: 512 Cov.: 32 AF XY: 0.0769 AC XY: 5725 AN XY: 74414

African (AFR) AF: 0.0647 AC: 2683 AN: 41496

American (AMR) AF: 0.113 AC: 1725 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3472

East Asian (EAS) AF: 0.178 AC: 926 AN: 5190

South Asian (SAS) AF: 0.170 AC: 822 AN: 4828

European-Finnish (FIN) AF: 0.0410 AC: 434 AN: 10574

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0607 AC: 4129 AN: 68026

Other (OTH) AF: 0.0742 AC: 157 AN: 2116

Alfa AF: 0.0681 Hom.: 586

Bravo AF: 0.0797

Asia WGS AF: 0.150 AC: 521 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	2.4
DANN	Benign	0.59
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs12072775; hg19: chr1-229272553;