dbSNP rs78825966: MIR557:n.68C>T (chr1-168375591-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000385239.1(MIR557):n.68C>T 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 0.0193 in 533,534 control chromosomes in the GnomAD database, including 822 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 0.051 ( 656 hom., cov: 32)

Exomes 𝑓: 0.0067 ( 166 hom. )

Consequence

MIR557
ENST00000385239.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.52

Publications

9 publications found

Variant links:

Genes affected

MIR557 (HGNC:32813): (microRNA 557) 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]

MIR557 links:

ENSG00000293102 (HGNC:):

ENSG00000293102 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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR557	NR_030284.1 link	n.68C>T		non_coding_transcript_exon_variant	Exon 1 of 1
MIR557	unassigned_transcript_238	n.8C>T		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR557	ENST00000385239.1 link	n.68C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000293102	ENST00000636624.1 link	n.1358-382C>T	intron_variant	Intron 2 of 3	5
ENSG00000307038	ENST00000823032.1 link	n.139-4018C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0508

AC:

7725

AN:

152112

Hom.:

653

Cov.:

show subpopulations

Gnomad AFR

AF:

0.175

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0224

Gnomad ASJ

AF:

0.00231

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00103

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000691

Gnomad OTH

AF:

0.0392

GnomAD2 exomes

AF:

0.0135

AC:

3358

AN:

249494

AF XY:

0.00983

show subpopulations

Gnomad AFR exome

AF:

0.179

Gnomad AMR exome

AF:

0.00826

Gnomad ASJ exome

AF:

0.00172

Gnomad EAS exome

AF:

0.000382

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000851

Gnomad OTH exome

AF:

0.00640

GnomAD4 exome

AF:

0.00673

AC:

2567

AN:

381304

Hom.:

166

Cov.:

AF XY:

0.00514

AC XY:

1116

AN XY:

217134

show subpopulations

African (AFR)

AF:

0.177

AC:

1848

AN:

10438

American (AMR)

AF:

0.00818

AC:

295

AN:

36044

Ashkenazi Jewish (ASJ)

AF:

0.000860

AC:

AN:

11628

East Asian (EAS)

AF:

0.000304

AC:

AN:

13164

South Asian (SAS)

AF:

0.000721

AC:

AN:

66578

European-Finnish (FIN)

AF:

0.00

AC:

AN:

32288

Middle Eastern (MID)

AF:

0.0173

AC:

AN:

2832

European-Non Finnish (NFE)

AF:

0.000793

AC:

152

AN:

191664

Other (OTH)

AF:

0.00966

AC:

161

AN:

16668

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

111

223

334

446

557

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

114

152

190

<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:

0.0509

AC:

7751

AN:

152230

Hom.:

656

Cov.:

AF XY:

0.0505

AC XY:

3760

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.175

AC:

7266

AN:

41498

American (AMR)

AF:

0.0224

AC:

343

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.00231

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5190

South Asian (SAS)

AF:

0.000829

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10608

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000691

AC:

AN:

68018

Other (OTH)

AF:

0.0388

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

330

660

989

1319

1649

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

216

288

360

<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:

0.0259

Hom.:

118

Bravo

AF:

0.0581

Asia WGS

AF:

0.0110

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.20

(source)

DANN

Benign

0.34

PhyloP100

-1.5

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