rs17459885

Variant names:

• chr12-30207946-T-C
• rs17459885
• ENST00000549055.1:n.127-496T>C

Variant summary

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

The ENST00000549055.1(ENSG00000257262):​n.127-496T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,282 control chromosomes in the GnomAD database, including 1,000 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 0.10 (1000 hom., cov: 33)
• Consequence: ENSG00000257262 ENST00000549055.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154
• Publications: 3 publications found

Genes affected

ENSG00000257262 (HGNC:):

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000549055.1. 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
	ENSG00000257262	ENST00000549055.1	TSL:3	n.127-496T>C		intron	N/A
	LINC02386	ENST00000824524.1		n.170-8307A>G		intron	N/A
	LINC02386	ENST00000824525.1		n.224-8307A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15952 AN: 152164 Hom.: 1000 Cov.: 33

Gnomad AFR AF: 0.0423

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0926

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.0358

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.105 AC: 15949 AN: 152282 Hom.: 1000 Cov.: 33 AF XY: 0.103 AC XY: 7660 AN XY: 74460

African (AFR) AF: 0.0422 AC: 1754 AN: 41570

American (AMR) AF: 0.103 AC: 1574 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0926 AC: 321 AN: 3468

East Asian (EAS) AF: 0.129 AC: 669 AN: 5176

South Asian (SAS) AF: 0.0358 AC: 173 AN: 4834

European-Finnish (FIN) AF: 0.143 AC: 1513 AN: 10606

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9489 AN: 68018

Other (OTH) AF: 0.125 AC: 264 AN: 2114

Alfa AF: 0.109 Hom.: 135

Bravo AF: 0.102

Asia WGS AF: 0.0830 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.7
DANN	Benign	0.59
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs17459885; hg19: chr12-30360879;