Genetic Variant ENST00000640185.1:n.61C>A (chr3-75630823-C-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000640185.1(MIR1324):n.61C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 69)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

MIR1324
ENST00000640185.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.351

Publications

2 publications found

Variant links:

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]

MIR1324 links:

ENSG00000293315 (HGNC:):

ENSG00000293315 links:

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

CLUHP10 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR1324	NR_031714.1 link	n.61C>A	non_coding_transcript_exon_variant	Exon 1 of 1
MIR1324	unassigned_transcript_644	n.1C>A	non_coding_transcript_exon_variant	Exon 1 of 1
CLUHP10		n.75630823C>A	intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR1324	ENST00000640185.1 link	n.61C>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000293315	ENST00000810254.1 link	n.202G>T	non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000293315	ENST00000810263.1 link	n.237G>T	non_coding_transcript_exon_variant	Exon 2 of 4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00

AC:

AN:

242370

AF XY:

0.00

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

382082

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

217550

African (AFR)

AF:

0.00

AC:

AN:

10418

American (AMR)

AF:

0.00

AC:

AN:

36268

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11740

East Asian (EAS)

AF:

0.00

AC:

AN:

13176

South Asian (SAS)

AF:

0.00

AC:

AN:

66732

European-Finnish (FIN)

AF:

0.00

AC:

AN:

32318

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2846

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

191888

Other (OTH)

AF:

0.00

AC:

AN:

16696

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

7.8

(source)

DANN

Benign

0.28

PhyloP100

0.35

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over