3-75630794-C-G

Variant names:

• chr3-75630794-C-G
• rs3008994
• ENST00000640185.1:n.32C>G

Variant summary

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

The NR_031714.1(MIR1324):​n.32C>G 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 (50 hom., cov: 62)
  • Exomes 𝑓: 0.25 (32 hom.)
  • Failed GnomAD Quality Control
• Consequence: MIR1324 NR_031714.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

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)

RPL23AP49 (HGNC:35689): (ribosomal protein L23a pseudogene 49)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR1324	NR_031714.1	n.32C>G		non_coding_transcript_exon_variant	Exon 1 of 1
CLUHP10		n.75630794C>G		intragenic_variant
MIR1324	unassigned_transcript_644	n.-29C>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR1324	ENST00000640185.1	n.32C>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
CLUHP10	ENST00000631979.1	n.340+23C>G		intron_variant	Intron 3 of 8	6
RPL23AP49	ENST00000638439.1	n.138-593G>C		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 43547 AN: 143996 Hom.: 50 Cov.: 62 FAILED QC

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.296

GnomAD4 exome AF: 0.254 AC: 78634 AN: 309494 Hom.: 32 Cov.: 0 AF XY: 0.259 AC XY: 45145 AN XY: 174510

Gnomad4 AFR exome AF: 0.296

Gnomad4 AMR exome AF: 0.240

Gnomad4 ASJ exome AF: 0.229

Gnomad4 EAS exome AF: 0.395

Gnomad4 SAS exome AF: 0.341

Gnomad4 FIN exome AF: 0.165

Gnomad4 NFE exome AF: 0.231

Gnomad4 OTH exome AF: 0.252

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.302 AC: 43562 AN: 144102 Hom.: 50 Cov.: 62 AF XY: 0.303 AC XY: 21276 AN XY: 70246

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.294

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	3.9
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3008994; hg19: chr3-75679945;