ENST00000652014.1:n.330+15308C>T

Variant names:

• chr12-90609119-C-T
• rs10492347
• ENST00000652014.1:n.330+15308C>T

Variant summary

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

The ENST00000652014.1(LINC02822):​n.330+15308C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,052 control chromosomes in the GnomAD database, including 3,171 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 0.18 (3171 hom., cov: 32)
• Consequence: LINC02822 ENST00000652014.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.848
• Publications: 2 publications found

Genes affected

LINC02822 (HGNC:54353): (long intergenic non-protein coding RNA 2822)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02822	XR_007063577.1	n.245+15308C>T		intron_variant	Intron 1 of 2
LINC02822	XR_429171.5	n.245+15308C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02822	ENST00000652014.1	n.330+15308C>T		intron_variant	Intron 2 of 5
LINC02822	ENST00000656065.1	n.423+15308C>T		intron_variant	Intron 2 of 4
LINC02822	ENST00000658113.2	n.494-369C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27314 AN: 151934 Hom.: 3170 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0970

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.00694

Gnomad SAS AF: 0.0804

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.180 AC: 27334 AN: 152052 Hom.: 3171 Cov.: 32 AF XY: 0.175 AC XY: 13014 AN XY: 74320

African (AFR) AF: 0.329 AC: 13612 AN: 41434

American (AMR) AF: 0.0969 AC: 1479 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 389 AN: 3466

East Asian (EAS) AF: 0.00696 AC: 36 AN: 5174

South Asian (SAS) AF: 0.0798 AC: 385 AN: 4822

European-Finnish (FIN) AF: 0.143 AC: 1509 AN: 10578

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9474 AN: 67998

Other (OTH) AF: 0.148 AC: 312 AN: 2110

Alfa AF: 0.148 Hom.: 1049

Bravo AF: 0.182

Asia WGS AF: 0.0630 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.60
DANN	Benign	0.43
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs10492347; hg19: chr12-91002896;