dbSNP rs9295535: MIR5689:n.19T>C (chr6-10439735-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 ENST00000581998.1(MIR5689):n.19T>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 0.2 in 147,136 control chromosomes in the GnomAD database, including 3,085 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 0.20 ( 3082 hom., cov: 23)

Exomes 𝑓: 0.20 ( 3 hom. )

Consequence

MIR5689
ENST00000581998.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.446

Publications

12 publications found

Variant links:

Genes affected

MIR5689 (HGNC:43479): (microRNA 5689) 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]

MIR5689 links:

TFAP2A-AS1 (HGNC:40579): (TFAP2A antisense RNA 1)

TFAP2A-AS1 links:

LINC00518 (HGNC:28626): (long intergenic non-protein coding RNA 518)

LINC00518 links:

MIR5689HG (HGNC:52007): (MIR5689 host gene)

MIR5689HG 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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR5689	NR_049872.1 link	n.19T>C	non_coding_transcript_exon_variant	Exon 1 of 1
MIR5689	unassigned_transcript_942	n.11T>C	non_coding_transcript_exon_variant	Exon 1 of 1
MIR5689HG	NR_132993.1 link	n.76+5331T>C	intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR5689	ENST00000581998.1 link	n.19T>C	non_coding_transcript_exon_variant	Exon 1 of 1	6
TFAP2A-AS1	ENST00000366312.2 link	n.76+5331T>C	intron_variant	Intron 1 of 3	3
TFAP2A-AS1	ENST00000449333.2 link	n.862+5331T>C	intron_variant	Intron 5 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.200

AC:

29338

AN:

146954

Hom.:

3085

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.134

Gnomad AMR

AF:

0.211

Gnomad ASJ

AF:

0.220

Gnomad EAS

AF:

0.286

Gnomad SAS

AF:

0.347

Gnomad FIN

AF:

0.168

Gnomad MID

AF:

0.219

Gnomad NFE

AF:

0.217

Gnomad OTH

AF:

0.201

GnomAD2 exomes

AF:

0.300

AC:

AN:

AF XY:

0.500

show subpopulations

Gnomad NFE exome

AF:

0.300

GnomAD4 exome

AF:

0.200

AC:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AF:

0.212

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.592

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:

0.200

AC:

29345

AN:

147076

Hom.:

3082

Cov.:

AF XY:

0.201

AC XY:

14397

AN XY:

71766

show subpopulations

African (AFR)

AF:

0.148

AC:

5979

AN:

40330

American (AMR)

AF:

0.211

AC:

3154

AN:

14952

Ashkenazi Jewish (ASJ)

AF:

0.220

AC:

749

AN:

3408

East Asian (EAS)

AF:

0.287

AC:

1354

AN:

4724

South Asian (SAS)

AF:

0.347

AC:

1552

AN:

4476

European-Finnish (FIN)

AF:

0.168

AC:

1675

AN:

9944

Middle Eastern (MID)

AF:

0.201

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.217

AC:

14297

AN:

66020

Other (OTH)

AF:

0.199

AC:

408

AN:

2046

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

1024

2047

3071

4094

5118

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

320

640

960

1280

1600

<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:

0.219

Hom.:

1708

Bravo

AF:

0.199

Asia WGS

AF:

0.282

AC:

981

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.0

(source)

DANN

Benign

0.70

PhyloP100

0.45

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