12-30215524-T-C

Variant names:

• chr12-30215524-T-C
• rs10843660
• ENST00000549055.1:n.258-2079T>C

Variant summary

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

The ENST00000549055.1(ENSG00000257262):​n.258-2079T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 151,792 control chromosomes in the GnomAD database, including 21,808 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 0.53 (21808 hom., cov: 33)
• Consequence: ENSG00000257262 ENST00000549055.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288
• Publications: 5 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.621 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.258-2079T>C		intron_variant	Intron 2 of 2	3
LINC02386	ENST00000824524.1	n.170-15885A>G		intron_variant	Intron 2 of 2
LINC02386	ENST00000824525.1	n.224-15885A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80855 AN: 151676 Hom.: 21787 Cov.: 33

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.533 AC: 80926 AN: 151792 Hom.: 21808 Cov.: 33 AF XY: 0.532 AC XY: 39448 AN XY: 74166

African (AFR) AF: 0.443 AC: 18340 AN: 41396

American (AMR) AF: 0.620 AC: 9455 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1976 AN: 3470

East Asian (EAS) AF: 0.639 AC: 3293 AN: 5152

South Asian (SAS) AF: 0.449 AC: 2164 AN: 4818

European-Finnish (FIN) AF: 0.522 AC: 5492 AN: 10514

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38352 AN: 67884

Other (OTH) AF: 0.548 AC: 1157 AN: 2110

Alfa AF: 0.562 Hom.: 102423

Bravo AF: 0.540

Asia WGS AF: 0.547 AC: 1901 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	2.3
DANN	Benign	0.47
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs10843660; hg19: chr12-30368457;