dbSNP rs9493099: MIR548H5:n.*32T>C (chr6-131792263-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 ENST00000580314.1(MIR548H5):n.*32T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 154,418 control chromosomes in the GnomAD database, including 7,203 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 0.28 ( 7091 hom., cov: 32)

Exomes 𝑓: 0.29 ( 112 hom. )

Consequence

MIR548H5
ENST00000580314.1 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0160

Publications

8 publications found

Variant links:

COSMIC-nc: COSV74123795

Genes affected

MIR548H5 (HGNC:41768): (microRNA 548h-5) 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]

MIR548H5 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=-0.86).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR548H5	NR_039610.1 link	n.*32T>C		downstream_gene_variant
MIR548H5	unassigned_transcript_1166	n.*68T>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR548H5	ENST00000580314.1 link	n.*32T>C		downstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

42388

AN:

152068

Hom.:

7084

Cov.:

show subpopulations

Gnomad AFR

AF:

0.124

Gnomad AMI

AF:

0.513

Gnomad AMR

AF:

0.422

Gnomad ASJ

AF:

0.230

Gnomad EAS

AF:

0.504

Gnomad SAS

AF:

0.544

Gnomad FIN

AF:

0.333

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.295

Gnomad OTH

AF:

0.299

GnomAD2 exomes

AF:

0.346

AC:

141

AN:

408

AF XY:

0.359

show subpopulations

Gnomad AFR exome

AF:

0.500

Gnomad ASJ exome

AF:

0.250

Gnomad FIN exome

AF:

0.500

Gnomad NFE exome

AF:

0.340

Gnomad OTH exome

AF:

0.333

GnomAD4 exome

AF:

0.289

AC:

646

AN:

2232

Hom.:

112

Cov.:

AF XY:

0.300

AC XY:

335

AN XY:

1118

show subpopulations

African (AFR)

AF:

0.158

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:

0.543

AC:

AN:

European-Finnish (FIN)

AF:

0.396

AC:

AN:

Middle Eastern (MID)

AF:

0.275

AC:

449

AN:

1632

European-Non Finnish (NFE)

AF:

0.344

AC:

AN:

180

Other (OTH)

AF:

0.263

AC:

AN:

190

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

106

132

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:

0.279

AC:

42405

AN:

152186

Hom.:

7091

Cov.:

AF XY:

0.289

AC XY:

21495

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.124

AC:

5160

AN:

41544

American (AMR)

AF:

0.422

AC:

6456

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.230

AC:

798

AN:

3468

East Asian (EAS)

AF:

0.504

AC:

2612

AN:

5180

South Asian (SAS)

AF:

0.544

AC:

2625

AN:

4826

European-Finnish (FIN)

AF:

0.333

AC:

3522

AN:

10576

Middle Eastern (MID)

AF:

0.262

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.295

AC:

20050

AN:

67988

Other (OTH)

AF:

0.302

AC:

638

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1496

2991

4487

5982

7478

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

446

892

1338

1784

2230

<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:

0.294

Hom.:

29054

Bravo

AF:

0.274

Asia WGS

AF:

0.502

AC:

1742

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

6.4

(source)

DANN

Benign

0.76

PhyloP100

-0.016

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

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over