dbSNP rs6997249: CCDC26:n.313-3429C>T (chr8-129484119-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NR_037457.1(MIR3686):n.24C>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 0.277 in 154,620 control chromosomes in the GnomAD database, including 6,402 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 ( 6295 hom., cov: 32)

Exomes 𝑓: 0.28 ( 107 hom. )

Consequence

MIR3686
NR_037457.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.03

Publications

11 publications found

Variant links:

Genes affected

CCDC26 (HGNC:28416): (CCDC26 long non-coding RNA)

CCDC26 links:

MIR3686 (HGNC:38887): (microRNA 3686) 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]

MIR3686 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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_037457.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
MIR3686	NR_037457.1	n.24C>T	non_coding_transcript_exon	Exon 1 of 1
CCDC26	NR_130917.1	n.313-3429C>T	intron	N/A
CCDC26	NR_130918.1	n.137+90763C>T	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
CCDC26	ENST00000446592.7	TSL:1	n.313-3429C>T	intron	N/A
CCDC26	ENST00000523151.6	TSL:1	n.135+90763C>T	intron	N/A
MIR3686	ENST00000577904.1	TSL:6	n.24C>T	non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.277

AC:

42090

AN:

151980

Hom.:

6293

Cov.:

show subpopulations

Gnomad AFR

AF:

0.209

Gnomad AMI

AF:

0.268

Gnomad AMR

AF:

0.275

Gnomad ASJ

AF:

0.241

Gnomad EAS

AF:

0.126

Gnomad SAS

AF:

0.174

Gnomad FIN

AF:

0.407

Gnomad MID

AF:

0.222

Gnomad NFE

AF:

0.320

Gnomad OTH

AF:

0.269

GnomAD2 exomes

AF:

0.298

AC:

1583

AN:

5318

AF XY:

0.315

show subpopulations

Gnomad AFR exome

AF:

0.217

Gnomad AMR exome

AF:

0.264

Gnomad ASJ exome

AF:

0.327

Gnomad EAS exome

AF:

0.0469

Gnomad NFE exome

AF:

0.312

Gnomad OTH exome

AF:

0.218

GnomAD4 exome

AF:

0.280

AC:

707

AN:

2522

Hom.:

107

Cov.:

AF XY:

0.298

AC XY:

391

AN XY:

1310

show subpopulations

African (AFR)

AF:

0.237

AC:

AN:

American (AMR)

AF:

0.125

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.208

AC:

AN:

European-Finnish (FIN)

AF:

0.400

AC:

171

AN:

428

Middle Eastern (MID)

AF:

0.257

AC:

402

AN:

1564

European-Non Finnish (NFE)

AF:

0.287

AC:

AN:

164

Other (OTH)

AF:

0.253

AC:

AN:

182

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

106

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:

0.277

AC:

42103

AN:

152098

Hom.:

6295

Cov.:

AF XY:

0.279

AC XY:

20775

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.209

AC:

8667

AN:

41498

American (AMR)

AF:

0.275

AC:

4195

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.241

AC:

835

AN:

3470

East Asian (EAS)

AF:

0.126

AC:

650

AN:

5176

South Asian (SAS)

AF:

0.174

AC:

841

AN:

4826

European-Finnish (FIN)

AF:

0.407

AC:

4294

AN:

10556

Middle Eastern (MID)

AF:

0.228

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.320

AC:

21743

AN:

67970

Other (OTH)

AF:

0.268

AC:

567

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

1565

3129

4694

6258

7823

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

424

848

1272

1696

2120

<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:

0.317

Hom.:

988

Bravo

AF:

0.266

Asia WGS

AF:

0.149

AC:

518

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.8

(source)

DANN

Benign

0.73

PhyloP100

1.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over