19-13836482-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The ENST00000385073.1(MIR27A):n.36C>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 0.0123 in 539,264 control chromosomes in the GnomAD database, including 66 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 0.012 ( 18 hom., cov: 32)

Exomes 𝑓: 0.013 ( 48 hom. )

Consequence

MIR27A
ENST00000385073.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.948

Publications

56 publications found

Variant links:

Genes affected

MIR27A (HGNC:31613): (microRNA 27a) 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]

MIR27A links:

MIR23AHG (HGNC:27620): (miR-23a/27a/24-2 cluster host gene)

MIR23AHG links:

MIR24-2 (HGNC:31608): (microRNA 24-2) 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]

MIR24-2 links:

MIR23A (HGNC:31605): (microRNA 23a) 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]

MIR23A links:

ENSG00000302686 (HGNC:):

ENSG00000302686 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=-0.73).

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0115 (1755/152338) while in subpopulation NFE AF = 0.0182 (1235/68024). AF 95% confidence interval is 0.0173. There are 18 homozygotes in GnomAd4. There are 821 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 18 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR27A	NR_029501.1 link	n.36C>T	non_coding_transcript_exon_variant	Exon 1 of 1
MIR23AHG	NR_036515.2 link	n.6437C>T	non_coding_transcript_exon_variant	Exon 1 of 1
MIR24-2	NR_029497.1 link	n.-123C>T	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR27A	ENST00000385073.1 link	n.36C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
MIR23AHG	ENST00000587762.2 link	n.6447C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
MIR24-2	ENST00000386972.1 link	n.-123C>T	upstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.0115

AC:

1752

AN:

152222

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00343

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0118

Gnomad ASJ

AF:

0.0323

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00414

Gnomad FIN

AF:

0.00179

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0181

Gnomad OTH

AF:

0.0177

GnomAD2 exomes

AF:

0.0119

AC:

2918

AN:

245456

AF XY:

0.0121

show subpopulations

Gnomad AFR exome

AF:

0.00279

Gnomad AMR exome

AF:

0.00867

Gnomad ASJ exome

AF:

0.0337

Gnomad EAS exome

AF:

0.0000551

Gnomad FIN exome

AF:

0.00214

Gnomad NFE exome

AF:

0.0176

Gnomad OTH exome

AF:

0.0168

GnomAD4 exome

AF:

0.0126

AC:

4860

AN:

386926

Hom.:

Cov.:

AF XY:

0.0124

AC XY:

2719

AN XY:

219826

show subpopulations

African (AFR)

AF:

0.00263

AC:

AN:

10638

American (AMR)

AF:

0.00874

AC:

315

AN:

36046

Ashkenazi Jewish (ASJ)

AF:

0.0347

AC:

409

AN:

11786

East Asian (EAS)

AF:

0.0000718

AC:

AN:

13926

South Asian (SAS)

AF:

0.00544

AC:

361

AN:

66338

European-Finnish (FIN)

AF:

0.00285

AC:

AN:

32960

Middle Eastern (MID)

AF:

0.0279

AC:

AN:

2870

European-Non Finnish (NFE)

AF:

0.0171

AC:

3333

AN:

195384

Other (OTH)

AF:

0.0141

AC:

239

AN:

16978

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

281

562

843

1124

1405

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:

0.0115

AC:

1755

AN:

152338

Hom.:

Cov.:

AF XY:

0.0110

AC XY:

821

AN XY:

74490

show subpopulations

African (AFR)

AF:

0.00342

AC:

142

AN:

41580

American (AMR)

AF:

0.0118

AC:

180

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0323

AC:

112

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5190

South Asian (SAS)

AF:

0.00414

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.00179

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0182

AC:

1235

AN:

68024

Other (OTH)

AF:

0.0180

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

171

256

342

427

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

<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:

0.0164

Hom.:

Bravo

AF:

0.0118

Asia WGS

AF:

0.00346

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

(source)

DANN

Benign

0.88

PhyloP100

0.95

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