dbSNP rs41280052: MIR184:n.39G>T (chr15-79209826-G-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The ENST00000384962.1(MIR184):n.39G>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 0.0104 in 518,594 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.011 ( 12 hom., cov: 32)

Exomes 𝑓: 0.010 ( 32 hom. )

Consequence

MIR184
ENST00000384962.1 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.615

Publications

14 publications found

Variant links:

Genes affected

MIR184 (HGNC:31555): (microRNA 184) 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 target mRNAs. This microRNA represents the most abundant miRNA in the corneal and lens epithelia of the eye and has been shown to interfere with target binding by another miRNA, miR-205. Through regulation of the VEGF and Akt signaling pathways, this microRNA may inhibit corneal angiogenesis. Mutations in the seed region of this microRNA cause familial keratoconus with cataract, also known as EDICT syndrome. [provided by RefSeq, Mar 2017]

MIR184 links:

ENSG00000292375 (HGNC:):

ENSG00000292375 links:

ANKRD34C-AS1 (HGNC:48618): (ANKRD34C antisense RNA 1)

ANKRD34C-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 15-79209826-G-T is Benign according to our data. Variant chr15-79209826-G-T is described in ClinVar as Benign. ClinVar VariationId is 1606846.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0109 (1660/152320) while in subpopulation NFE AF = 0.0171 (1162/68030). AF 95% confidence interval is 0.0163. There are 12 homozygotes in GnomAd4. There are 774 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High AC in GnomAd4 at 1660 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR184	NR_029705.1 link	n.39G>T	non_coding_transcript_exon_variant	Exon 1 of 1
ANKRD34C-AS1	NR_038997.1 link	n.298-17724C>A	intron_variant	Intron 1 of 1
MIR184	unassigned_transcript_2726	n.-14G>T	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR184	ENST00000384962.1 link	n.39G>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000292375	ENST00000711326.1 link	n.424G>T	non_coding_transcript_exon_variant	Exon 1 of 2
ANKRD34C-AS1	ENST00000559225.3 link	n.470+3361C>A	intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes

AF:

0.0109

AC:

1660

AN:

152202

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00275

Gnomad AMI

AF:

0.0603

Gnomad AMR

AF:

0.00713

Gnomad ASJ

AF:

0.00518

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.0169

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0171

Gnomad OTH

AF:

0.00766

GnomAD2 exomes

AF:

0.00986

AC:

2469

AN:

250520

AF XY:

0.0100

show subpopulations

Gnomad AFR exome

AF:

0.00223

Gnomad AMR exome

AF:

0.00426

Gnomad ASJ exome

AF:

0.00637

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0173

Gnomad NFE exome

AF:

0.0156

Gnomad OTH exome

AF:

0.00965

GnomAD4 exome

AF:

0.0102

AC:

3723

AN:

366274

Hom.:

Cov.:

AF XY:

0.00961

AC XY:

2010

AN XY:

209182

show subpopulations

African (AFR)

AF:

0.00300

AC:

AN:

10344

American (AMR)

AF:

0.00415

AC:

150

AN:

36180

Ashkenazi Jewish (ASJ)

AF:

0.00631

AC:

AN:

11410

East Asian (EAS)

AF:

0.00

AC:

AN:

12982

South Asian (SAS)

AF:

0.000706

AC:

AN:

65134

European-Finnish (FIN)

AF:

0.0165

AC:

524

AN:

31740

Middle Eastern (MID)

AF:

0.00254

AC:

AN:

2754

European-Non Finnish (NFE)

AF:

0.0152

AC:

2736

AN:

179956

Other (OTH)

AF:

0.00995

AC:

157

AN:

15774

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.455

Heterozygous variant carriers

153

306

460

613

766

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:

0.0109

AC:

1660

AN:

152320

Hom.:

Cov.:

AF XY:

0.0104

AC XY:

774

AN XY:

74486

show subpopulations

African (AFR)

AF:

0.00274

AC:

114

AN:

41570

American (AMR)

AF:

0.00712

AC:

109

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.00518

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5186

South Asian (SAS)

AF:

0.00145

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.0169

AC:

179

AN:

10610

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0171

AC:

1162

AN:

68030

Other (OTH)

AF:

0.00758

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

159

239

318

398

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

110

<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:

0.0122

Hom.:

Bravo

AF:

0.00958

Asia WGS

AF:

0.000866

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jan 23, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

(source)

DANN

Benign

0.88

PhyloP100

0.61

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over