ENST00000640185.1:n.32C>A

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000640185.1(MIR1324):​n.32C>A 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 0.00102 in 152,038 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0010 (0 hom., cov: 62)
  • Exomes 𝑓: 0.0013 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MIR1324 ENST00000640185.1 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 Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00103 AC: 156 AN: 151920 Hom.: 0 Cov.: 62

Gnomad AFR AF: 0.000822

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000525

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00686

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00103

Gnomad OTH AF: 0.00240

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00134 AC: 498 AN: 372156 Hom.: 0 Cov.: 0 AF XY: 0.00160 AC XY: 339 AN XY: 211510

Gnomad4 AFR exome AF: 0.000294

Gnomad4 AMR exome AF: 0.000172

Gnomad4 ASJ exome AF: 0.000613

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00496

Gnomad4 FIN exome AF: 0.000159

Gnomad4 NFE exome AF: 0.000684

Gnomad4 OTH exome AF: 0.00111

GnomAD4 genome AF: 0.00102 AC: 155 AN: 152038 Hom.: 0 Cov.: 62 AF XY: 0.00106 AC XY: 79 AN XY: 74318

Gnomad4 AFR AF: 0.000820

Gnomad4 AMR AF: 0.000524

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00665

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00103

Gnomad4 OTH AF: 0.00238

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	3.8
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;