Variant 14-101056219-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_036133.1(MIR323B):n.1T>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 0.246 in 532,696 control chromosomes in the GnomAD database, including 20,747 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 0.19 ( 4156 hom., cov: 32)

Exomes 𝑓: 0.27 ( 16591 hom. )

Consequence

MIR323B
NR_036133.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.212

Variant links:

Genes affected

MIR323B (HGNC:38349): (microRNA 323b) 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]

MIR323B links:

MEG9 (HGNC:43874): (maternally expressed 9)

MEG9 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR323B	NR_036133.1 linkuse as main transcript	n.1T>C		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons
MIR323B	ENST00000385269.2 linkuse as main transcript	n.1T>C	non_coding_transcript_exon_variant	1/1
MEG9	ENST00000699461.1 linkuse as main transcript	n.356T>C	non_coding_transcript_exon_variant	3/7
MEG9	ENST00000699460.1 linkuse as main transcript	n.2751T>C	non_coding_transcript_exon_variant	17/17

Frequencies

GnomAD3 genomes

AF:

0.193

AC:

29390

AN:

152090

Hom.:

4157

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0507

Gnomad AMI

AF:

0.158

Gnomad AMR

AF:

0.303

Gnomad ASJ

AF:

0.184

Gnomad EAS

AF:

0.683

Gnomad SAS

AF:

0.367

Gnomad FIN

AF:

0.200

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.205

Gnomad OTH

AF:

0.211

GnomAD3 exomes

AF:

0.278

AC:

69625

AN:

250342

Hom.:

12840

AF XY:

0.277

AC XY:

37514

AN XY:

135520

show subpopulations

Gnomad AFR exome

AF:

0.0473

Gnomad AMR exome

AF:

0.441

Gnomad ASJ exome

AF:

0.184

Gnomad EAS exome

AF:

0.678

Gnomad SAS exome

AF:

0.348

Gnomad FIN exome

AF:

0.203

Gnomad NFE exome

AF:

0.202

Gnomad OTH exome

AF:

0.242

GnomAD4 exome

AF:

0.267

AC:

101402

AN:

380488

Hom.:

16591

Cov.:

AF XY:

0.270

AC XY:

58460

AN XY:

216726

show subpopulations

Gnomad4 AFR exome

AF:

0.0494

Gnomad4 AMR exome

AF:

0.443

Gnomad4 ASJ exome

AF:

0.182

Gnomad4 EAS exome

AF:

0.693

Gnomad4 SAS exome

AF:

0.343

Gnomad4 FIN exome

AF:

0.202

Gnomad4 NFE exome

AF:

0.209

Gnomad4 OTH exome

AF:

0.226

GnomAD4 genome

AF:

0.193

AC:

29393

AN:

152208

Hom.:

4156

Cov.:

AF XY:

0.202

AC XY:

15040

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.0505

Gnomad4 AMR

AF:

0.304

Gnomad4 ASJ

AF:

0.184

Gnomad4 EAS

AF:

0.684

Gnomad4 SAS

AF:

0.365

Gnomad4 FIN

AF:

0.200

Gnomad4 NFE

AF:

0.205

Gnomad4 OTH

AF:

0.212

Alfa

AF:

0.181

Hom.:

1297

Bravo

AF:

0.197

Asia WGS

AF:

0.466

AC:

1620

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

8.4

DANN

Benign

0.59

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