rs10506063

Variant names:

• chr12-30256816-G-A
• rs10506063
• ENST00000551202.1:n.103-12411C>T

Variant summary

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

The ENST00000551202.1(LINC02386):​n.103-12411C>T variant causes a intron 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 ENST00000551202.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02386	NR_183469.1	n.146-12411C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02386	ENST00000551202.1	n.103-12411C>T		intron_variant	Intron 2 of 4	3
LINC02386	ENST00000552182.7	n.98-12411C>T		intron_variant	Intron 1 of 3	3
LINC02386	ENST00000655472.2	n.153-12411C>T		intron_variant	Intron 2 of 4

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

African (AFR) AF: 0.0256 AC: 1065 AN: 41534

American (AMR) AF: 0.0230 AC: 352 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0421 AC: 146 AN: 3466

East Asian (EAS) AF: 0.108 AC: 555 AN: 5142

South Asian (SAS) AF: 0.0424 AC: 204 AN: 4812

European-Finnish (FIN) AF: 0.0421 AC: 446 AN: 10598

Middle Eastern (MID) AF: 0.0205 AC: 6 AN: 292

European-Non Finnish (NFE) AF: 0.0331 AC: 2250 AN: 68016

Other (OTH) AF: 0.0255 AC: 54 AN: 2116

Alfa AF: 0.0326 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
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs10506063; hg19: chr12-30409749;