rs10492347

chr12-90609119-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000652014.1(LINC02822):n.330+15308C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.848

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02822	XR_429171.5	n.245+15308C>T		intron_variant, non_coding_transcript_variant
LINC02822	XR_007063577.1	n.245+15308C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02822	ENST00000652014.1	n.330+15308C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.0969

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.00696

Gnomad4 SAS AF: 0.0798

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.148

Alfa AF: 0.149 Hom.: 952

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492347; hg19: chr12-91002896;