rs3008994

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr3-75630794-C-A
• chr3-75630794-C-G
• chr3-75630794-C-T

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 1 publications found

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]

ENSG00000293315 (HGNC:):

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

ACMG classification

Our verdict: Likely_benign. The variant received -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
ENSG00000293315	ENST00000810254.1	n.231G>T		non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000293315	ENST00000810263.1	n.266G>T		non_coding_transcript_exon_variant	Exon 2 of 4

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

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000294 AC: 3 AN: 10202

American (AMR) AF: 0.000172 AC: 6 AN: 34890

Ashkenazi Jewish (ASJ) AF: 0.000613 AC: 7 AN: 11410

East Asian (EAS) AF: 0.00 AC: 0 AN: 12876

South Asian (SAS) AF: 0.00496 AC: 324 AN: 65272

European-Finnish (FIN) AF: 0.000159 AC: 5 AN: 31466

Middle Eastern (MID) AF: 0.00254 AC: 7 AN: 2754

European-Non Finnish (NFE) AF: 0.000684 AC: 128 AN: 187006

Other (OTH) AF: 0.00111 AC: 18 AN: 16280

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000820 AC: 34 AN: 41480

American (AMR) AF: 0.000524 AC: 8 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.00173 AC: 6 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.00665 AC: 32 AN: 4810

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10610

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00103 AC: 70 AN: 67920

Other (OTH) AF: 0.00238 AC: 5 AN: 2102

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 0

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
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs3008994; hg19: chr3-75679945;