12-30216329-A-G

Variant names:

• chr12-30216329-A-G
• rs9669515
• ENST00000549055.1:n.258-1274A>G

Variant summary

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

The ENST00000549055.1(ENSG00000257262):​n.258-1274A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 152,140 control chromosomes in the GnomAD database, including 45,223 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 0.77 (45223 hom., cov: 32)
• Consequence: ENSG00000257262 ENST00000549055.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515
• Publications: 1 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257262	ENST00000549055.1	n.258-1274A>G		intron_variant	Intron 2 of 2	3
LINC02386	ENST00000824524.1	n.170-16690T>C		intron_variant	Intron 2 of 2
LINC02386	ENST00000824525.1	n.224-16690T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116338 AN: 152020 Hom.: 45151 Cov.: 32

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.766 AC: 116473 AN: 152140 Hom.: 45223 Cov.: 32 AF XY: 0.764 AC XY: 56823 AN XY: 74356

African (AFR) AF: 0.900 AC: 37385 AN: 41534

American (AMR) AF: 0.773 AC: 11818 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2482 AN: 3470

East Asian (EAS) AF: 0.831 AC: 4289 AN: 5162

South Asian (SAS) AF: 0.734 AC: 3537 AN: 4816

European-Finnish (FIN) AF: 0.678 AC: 7164 AN: 10568

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47275 AN: 67974

Other (OTH) AF: 0.758 AC: 1603 AN: 2116

Alfa AF: 0.689 Hom.: 6563

Bravo AF: 0.779

Asia WGS AF: 0.799 AC: 2776 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	2.1
DANN	Benign	0.23
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs9669515; hg19: chr12-30369262;