rs10492347

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652014.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02822	ENST00000652014.1		n.330+15308C>T		intron	N/A
	LINC02822	ENST00000656065.1		n.423+15308C>T		intron	N/A
	LINC02822	ENST00000658113.2		n.494-369C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10492347;

hg19: chr12-91002896;