ENST00000551202.1:n.103-13961C>A

Variant names:

• chr12-30258366-G-T
• rs1835255
• ENST00000551202.1:n.103-13961C>A

Variant summary

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

The ENST00000551202.1(LINC02386):​n.103-13961C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 151,958 control chromosomes in the GnomAD database, including 11,128 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 0.37 (11128 hom., cov: 32)
• Consequence: LINC02386 ENST00000551202.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798
• Publications: 0 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000551202.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02386	NR_183469.1		n.146-13961C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02386	ENST00000551202.1	TSL:3	n.103-13961C>A		intron	N/A
	LINC02386	ENST00000552182.7	TSL:3	n.98-13961C>A		intron	N/A
	LINC02386	ENST00000655472.2		n.153-13961C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55842 AN: 151840 Hom.: 11122 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.368 AC: 55870 AN: 151958 Hom.: 11128 Cov.: 32 AF XY: 0.374 AC XY: 27766 AN XY: 74290

African (AFR) AF: 0.230 AC: 9551 AN: 41454

American (AMR) AF: 0.481 AC: 7349 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1229 AN: 3466

East Asian (EAS) AF: 0.683 AC: 3515 AN: 5150

South Asian (SAS) AF: 0.501 AC: 2414 AN: 4820

European-Finnish (FIN) AF: 0.381 AC: 4030 AN: 10568

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.391 AC: 26531 AN: 67918

Other (OTH) AF: 0.368 AC: 775 AN: 2106

Alfa AF: 0.383 Hom.: 5856

Bravo AF: 0.368

Asia WGS AF: 0.552 AC: 1921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.34
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs1835255; hg19: chr12-30411299;