rs3008993

Positions:

• chr3-75630855-T-C

Variant summary

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

The NR_031714.1(MIR1324):​n.93T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.30 (34 hom., cov: 65)
  • Exomes 𝑓: 0.26 (35 hom.)
  • Failed GnomAD Quality Control
• Consequence: MIR1324 NR_031714.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620

Genes affected

MIR1324 (HGNC:35377): (microRNA 1324) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

CLUHP10 (HGNC:51574): (clustered mitochondria homolog pseudogene 10)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR1324	NR_031714.1	n.93T>C		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR1324	ENST00000640185.1	n.93T>C		non_coding_transcript_exon_variant	1/1
CLUHP10	ENST00000631979.1	n.340+84T>C		intron_variant, non_coding_transcript_variant
	ENST00000638439.1	n.138-654A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 41942 AN: 139478 Hom.: 34 Cov.: 65 FAILED QC

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.297

GnomAD4 exome AF: 0.259 AC: 80041 AN: 309326 Hom.: 35 Cov.: 0 AF XY: 0.264 AC XY: 45967 AN XY: 174176

Gnomad4 AFR exome AF: 0.314

Gnomad4 AMR exome AF: 0.247

Gnomad4 ASJ exome AF: 0.236

Gnomad4 EAS exome AF: 0.398

Gnomad4 SAS exome AF: 0.352

Gnomad4 FIN exome AF: 0.159

Gnomad4 NFE exome AF: 0.235

Gnomad4 OTH exome AF: 0.256

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.301 AC: 41960 AN: 139574 Hom.: 34 Cov.: 65 AF XY: 0.301 AC XY: 20475 AN XY: 67976

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.294

Alfa AF: 0.305 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	12
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3008993; hg19: chr3-75680006;