dbSNP rs12410786: MIR29B2CHG:n.662+3145A>T (chr1-207802860-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000710901.1(MIR29B2CHG):n.662+3145A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 157,864 control chromosomes in the GnomAD database, including 7,577 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 0.29 ( 6938 hom., cov: 32)

Exomes 𝑓: 0.47 ( 639 hom. )

Consequence

MIR29B2CHG
ENST00000710901.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.308

Publications

5 publications found

Variant links:

Genes affected

MIR29B2CHG (HGNC:32018): (MIR29B2 and MIR29C host gene)

MIR29B2CHG 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=-0.75).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR29B2CHG	NR_135298.1 link	n.922-198A>T		intron_variant	Intron 4 of 4
MIR29B2CHG	NR_135299.1 link	n.1107-198A>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
MIR29B2CHG	ENST00000710901.1 link	n.662+3145A>T	intron_variant	Intron 5 of 5
MIR29B2CHG	ENST00000710902.1 link	n.569+13069A>T	intron_variant	Intron 4 of 4
MIR29B2CHG	ENST00000710903.1 link	n.757+13069A>T	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.290

AC:

44100

AN:

152026

Hom.:

6925

Cov.:

show subpopulations

Gnomad AFR

AF:

0.201

Gnomad AMI

AF:

0.271

Gnomad AMR

AF:

0.409

Gnomad ASJ

AF:

0.256

Gnomad EAS

AF:

0.0983

Gnomad SAS

AF:

0.234

Gnomad FIN

AF:

0.384

Gnomad MID

AF:

0.218

Gnomad NFE

AF:

0.325

Gnomad OTH

AF:

0.264

GnomAD4 exome

AF:

0.469

AC:

2685

AN:

5722

Hom.:

639

Cov.:

AF XY:

0.467

AC XY:

1452

AN XY:

3108

show subpopulations

African (AFR)

AF:

0.330

AC:

AN:

106

American (AMR)

AF:

0.599

AC:

309

AN:

516

Ashkenazi Jewish (ASJ)

AF:

0.331

AC:

AN:

160

East Asian (EAS)

AF:

0.225

AC:

AN:

178

South Asian (SAS)

AF:

0.372

AC:

298

AN:

802

European-Finnish (FIN)

AF:

0.539

AC:

138

AN:

256

Middle Eastern (MID)

AF:

0.269

AC:

AN:

European-Non Finnish (NFE)

AF:

0.491

AC:

1681

AN:

3422

Other (OTH)

AF:

0.484

AC:

124

AN:

256

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.578

Heterozygous variant carriers

130

194

259

324

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:

0.290

AC:

44116

AN:

152142

Hom.:

6938

Cov.:

AF XY:

0.293

AC XY:

21803

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.201

AC:

8329

AN:

41532

American (AMR)

AF:

0.410

AC:

6268

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.256

AC:

890

AN:

3470

East Asian (EAS)

AF:

0.0982

AC:

508

AN:

5174

South Asian (SAS)

AF:

0.234

AC:

1129

AN:

4822

European-Finnish (FIN)

AF:

0.384

AC:

4050

AN:

10548

Middle Eastern (MID)

AF:

0.214

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.325

AC:

22081

AN:

67986

Other (OTH)

AF:

0.260

AC:

551

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1584

3168

4751

6335

7919

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

450

900

1350

1800

2250

<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:

0.305

Hom.:

899

Bravo

AF:

0.290

Asia WGS

AF:

0.167

AC:

585

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

5.7

(source)

DANN

Benign

0.84

PhyloP100

0.31

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