rs10506063

chr12-30256816-G-A

Variant summary

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

The NR_183469.1(LINC02386):n.146-12411C>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 0.0338 in 152,160 control chromosomes in the GnomAD database, including 106 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 0.034 (106 hom., cov: 32)
• Consequence: LINC02386 NR_183469.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595

Genes affected

LINC02386 (HGNC:53312): (long intergenic non-protein coding RNA 2386)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02386	NR_183469.1	n.146-12411C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02386	ENST00000663022.1	n.146-12411C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0338 AC: 5145 AN: 152042 Hom.: 106 Cov.: 32

Gnomad AFR AF: 0.0256

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0231

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.0426

Gnomad FIN AF: 0.0421

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.0331

Gnomad OTH AF: 0.0253

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

GnomAD4 genome AF: 0.0338 AC: 5147 AN: 152160 Hom.: 106 Cov.: 32 AF XY: 0.0348 AC XY: 2587 AN XY: 74378

Gnomad4 AFR AF: 0.0256

Gnomad4 AMR AF: 0.0230

Gnomad4 ASJ AF: 0.0421

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.0424

Gnomad4 FIN AF: 0.0421

Gnomad4 NFE AF: 0.0331

Gnomad4 OTH AF: 0.0255

Alfa AF: 0.0330 Hom.: 14

Bravo AF: 0.0328

Asia WGS AF: 0.0660 AC: 230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.018
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506063; hg19: chr12-30409749;