Variant 8-1817259-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_030326.1(MIR596):n.29T>C 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 0.085 in 516,166 control chromosomes in the GnomAD database, including 2,251 homozygotes. 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 0.094 ( 689 hom., cov: 33)

Exomes 𝑓: 0.081 ( 1562 hom. )

Consequence

MIR596
NR_030326.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0480

Variant links:

Genes affected

MIR596 (HGNC:32852): (microRNA 596) 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]

MIR596 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR596	NR_030326.1 linkuse as main transcript	n.29T>C		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR596	ENST00000385091.1 linkuse as main transcript	n.29T>C		mature_miRNA_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.0944

AC:

14367

AN:

152144

Hom.:

689

Cov.:

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.0782

Gnomad ASJ

AF:

0.0942

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.0130

Gnomad FIN

AF:

0.119

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.104

Gnomad OTH

AF:

0.102

GnomAD3 exomes

AF:

0.0813

AC:

19664

AN:

242000

Hom.:

992

AF XY:

0.0794

AC XY:

10419

AN XY:

131280

show subpopulations

Gnomad AFR exome

AF:

0.104

Gnomad AMR exome

AF:

0.0539

Gnomad ASJ exome

AF:

0.0969

Gnomad EAS exome

AF:

0.000170

Gnomad SAS exome

AF:

0.0144

Gnomad FIN exome

AF:

0.106

Gnomad NFE exome

AF:

0.109

Gnomad OTH exome

AF:

0.0967

GnomAD4 exome

AF:

0.0811

AC:

29522

AN:

363904

Hom.:

1562

Cov.:

AF XY:

0.0761

AC XY:

15654

AN XY:

205804

show subpopulations

Gnomad4 AFR exome

AF:

0.0953

Gnomad4 AMR exome

AF:

0.0544

Gnomad4 ASJ exome

AF:

0.0966

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0153

Gnomad4 FIN exome

AF:

0.106

Gnomad4 NFE exome

AF:

0.108

Gnomad4 OTH exome

AF:

0.0901

GnomAD4 genome

AF:

0.0944

AC:

14368

AN:

152262

Hom.:

689

Cov.:

AF XY:

0.0932

AC XY:

6941

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.101

Gnomad4 AMR

AF:

0.0781

Gnomad4 ASJ

AF:

0.0942

Gnomad4 EAS

AF:

0.000772

Gnomad4 SAS

AF:

0.0133

Gnomad4 FIN

AF:

0.119

Gnomad4 NFE

AF:

0.104

Gnomad4 OTH

AF:

0.100

Alfa

AF:

0.102

Hom.:

346

Bravo

AF:

0.0929

Asia WGS

AF:

0.0180

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.4

DANN

Benign

0.24

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over