rs12894467

Positions:

• chr14-101041390-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_030582.1(MIR300):​n.28C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 533,582 control chromosomes in the GnomAD database, including 68,634 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 0.51 (20245 hom., cov: 32)
  • Exomes 𝑓: 0.49 (48389 hom.)
• Consequence: MIR300 NR_030582.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

Genes affected

MIR300 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR300	NR_030582.1	n.28C>T		non_coding_transcript_exon_variant	1/1
MIR300	unassigned_transcript_2409	n.-24C>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR300	ENST00000401138.1	n.28C>T		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76841 AN: 151932 Hom.: 20221 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.508

GnomAD3 exomes AF: 0.511 AC: 127914 AN: 250308 Hom.: 34489 AF XY: 0.505 AC XY: 68426 AN XY: 135508

Gnomad AFR exome AF: 0.601

Gnomad AMR exome AF: 0.616

Gnomad ASJ exome AF: 0.440

Gnomad EAS exome AF: 0.771

Gnomad SAS exome AF: 0.572

Gnomad FIN exome AF: 0.504

Gnomad NFE exome AF: 0.417

Gnomad OTH exome AF: 0.474

GnomAD4 exome AF: 0.492 AC: 187710 AN: 381532 Hom.: 48389 Cov.: 0 AF XY: 0.493 AC XY: 107163 AN XY: 217228

Gnomad4 AFR exome AF: 0.591

Gnomad4 AMR exome AF: 0.618

Gnomad4 ASJ exome AF: 0.440

Gnomad4 EAS exome AF: 0.780

Gnomad4 SAS exome AF: 0.561

Gnomad4 FIN exome AF: 0.499

Gnomad4 NFE exome AF: 0.422

Gnomad4 OTH exome AF: 0.474

GnomAD4 genome AF: 0.506 AC: 76917 AN: 152050 Hom.: 20245 Cov.: 32 AF XY: 0.513 AC XY: 38105 AN XY: 74314

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.507

Alfa AF: 0.454 Hom.: 7000

Bravo AF: 0.513

Asia WGS AF: 0.671 AC: 2329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.3
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12894467; hg19: chr14-101507727; COSMIC: COSV62999658;