dbSNP rs67106263: MIR3144:n.60G>A (chr6-120015238-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000579460.1(MIR3144):n.60G>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 0.219 in 152,536 control chromosomes in the GnomAD database, including 3,913 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 0.22 ( 3886 hom., cov: 31)

Exomes 𝑓: 0.22 ( 27 hom. )

Consequence

MIR3144
ENST00000579460.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.123

Publications

10 publications found

Variant links:

Genes affected

MIR3144 (HGNC:38331): (microRNA 3144) 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]

MIR3144 links:

ENSG00000308468 (HGNC:):

ENSG00000308468 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

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

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR3144	NR_036098.1 link	n.60G>A	non_coding_transcript_exon_variant	Exon 1 of 1
MIR3144	unassigned_transcript_1163	n.13G>A	non_coding_transcript_exon_variant	Exon 1 of 1
MIR3144	unassigned_transcript_1162	n.*26G>A	downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR3144	ENST00000579460.1 link	n.60G>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000308468	ENST00000834274.1 link	n.94+9422G>A	intron_variant	Intron 1 of 4
ENSG00000308468	ENST00000834275.1 link	n.94+9422G>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.219

AC:

33144

AN:

151418

Hom.:

3875

Cov.:

show subpopulations

Gnomad AFR

AF:

0.190

Gnomad AMI

AF:

0.480

Gnomad AMR

AF:

0.323

Gnomad ASJ

AF:

0.259

Gnomad EAS

AF:

0.129

Gnomad SAS

AF:

0.180

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.226

Gnomad OTH

AF:

0.218

GnomAD2 exomes

AF:

0.229

AC:

1450

AN:

6334

AF XY:

0.226

show subpopulations

Gnomad AFR exome

AF:

0.198

Gnomad AMR exome

AF:

0.328

Gnomad ASJ exome

AF:

0.268

Gnomad EAS exome

AF:

0.100

Gnomad NFE exome

AF:

0.229

Gnomad OTH exome

AF:

0.261

GnomAD4 exome

AF:

0.222

AC:

222

AN:

1002

Hom.:

Cov.:

AF XY:

0.199

AC XY:

112

AN XY:

564

show subpopulations

African (AFR)

AF:

0.214

AC:

AN:

American (AMR)

AF:

0.250

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.222

AC:

AN:

European-Finnish (FIN)

AF:

0.167

AC:

AN:

424

Middle Eastern (MID)

AF:

0.289

AC:

AN:

318

European-Non Finnish (NFE)

AF:

0.244

AC:

AN:

168

Other (OTH)

AF:

0.167

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.541

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.219

AC:

33188

AN:

151534

Hom.:

3886

Cov.:

AF XY:

0.218

AC XY:

16116

AN XY:

74014

show subpopulations

African (AFR)

AF:

0.191

AC:

7884

AN:

41366

American (AMR)

AF:

0.324

AC:

4928

AN:

15214

Ashkenazi Jewish (ASJ)

AF:

0.259

AC:

898

AN:

3464

East Asian (EAS)

AF:

0.129

AC:

666

AN:

5164

South Asian (SAS)

AF:

0.180

AC:

864

AN:

4806

European-Finnish (FIN)

AF:

0.163

AC:

1705

AN:

10458

Middle Eastern (MID)

AF:

0.218

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.226

AC:

15294

AN:

67768

Other (OTH)

AF:

0.215

AC:

450

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1309

2618

3926

5235

6544

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

356

712

1068

1424

1780

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.210

Hom.:

463

Bravo

AF:

0.231

Asia WGS

AF:

0.156

AC:

547

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

7.6

(source)

DANN

Benign

0.78

PhyloP100

0.12

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over