Genetic Variant MIR5197:n.9T>C (chr5-143679868-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000583721.1(MIR5197):n.9T>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 0.269 in 154,056 control chromosomes in the GnomAD database, including 5,817 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 0.27 ( 5682 hom., cov: 32)

Exomes 𝑓: 0.36 ( 135 hom. )

Consequence

MIR5197
ENST00000583721.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.319

Publications

19 publications found

Variant links:

Genes affected

MIR5197 (HGNC:43450): (microRNA 5197) 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]

MIR5197 links:

ENSG00000249881 (HGNC:):

ENSG00000249881 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=-0.78).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR5197	NR_049829.1 link	n.9T>C	non_coding_transcript_exon_variant	Exon 1 of 1
MIR5197	unassigned_transcript_871	n.-18T>C	upstream_gene_variant
MIR5197	unassigned_transcript_872	n.-55T>C	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR5197	ENST00000583721.1 link	n.9T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000249881	ENST00000503323.1 link	n.379+7171T>C		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes

AF:

0.268

AC:

40757

AN:

151976

Hom.:

5672

Cov.:

show subpopulations

Gnomad AFR

AF:

0.321

Gnomad AMI

AF:

0.367

Gnomad AMR

AF:

0.253

Gnomad ASJ

AF:

0.339

Gnomad EAS

AF:

0.380

Gnomad SAS

AF:

0.308

Gnomad FIN

AF:

0.157

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.241

Gnomad OTH

AF:

0.267

GnomAD2 exomes

AF:

0.219

AC:

AN:

AF XY:

0.156

show subpopulations

Gnomad AFR exome

AF:

0.250

Gnomad ASJ exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.231

Gnomad OTH exome

AF:

0.250

GnomAD4 exome

AF:

0.360

AC:

706

AN:

1962

Hom.:

135

Cov.:

AF XY:

0.365

AC XY:

360

AN XY:

986

show subpopulations

African (AFR)

AF:

0.394

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.314

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.357

AC:

580

AN:

1626

European-Non Finnish (NFE)

AF:

0.400

AC:

AN:

Other (OTH)

AF:

0.401

AC:

AN:

172

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

125

156

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.268

AC:

40800

AN:

152094

Hom.:

5682

Cov.:

AF XY:

0.267

AC XY:

19884

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.321

AC:

13324

AN:

41492

American (AMR)

AF:

0.253

AC:

3865

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.339

AC:

1177

AN:

3470

East Asian (EAS)

AF:

0.381

AC:

1963

AN:

5158

South Asian (SAS)

AF:

0.307

AC:

1477

AN:

4814

European-Finnish (FIN)

AF:

0.157

AC:

1658

AN:

10590

Middle Eastern (MID)

AF:

0.259

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.241

AC:

16361

AN:

67982

Other (OTH)

AF:

0.268

AC:

565

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1507

3014

4522

6029

7536

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

428

856

1284

1712

2140

<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:

0.124

Hom.:

193

Bravo

AF:

0.280

Asia WGS

AF:

0.335

AC:

1163

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

5.5

(source)

DANN

Benign

0.67

PhyloP100

0.32

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