Genetic Variant ENST00000710901.1:n.662+3074C>G (chr1-207802931-G-C) – 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+3074C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,234 control chromosomes in the GnomAD database, including 9,229 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 0.33 ( 9217 hom., cov: 32)

Exomes 𝑓: 0.35 ( 12 hom. )

Consequence

MIR29B2CHG
ENST00000710901.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.742

Publications

6 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=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR29B2CHG	NR_135298.1 link	n.922-269C>G		intron_variant	Intron 4 of 4
MIR29B2CHG	NR_135299.1 link	n.1107-269C>G		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
MIR29B2CHG	ENST00000710901.1 link	n.662+3074C>G	intron_variant	Intron 5 of 5
MIR29B2CHG	ENST00000710902.1 link	n.569+12998C>G	intron_variant	Intron 4 of 4
MIR29B2CHG	ENST00000710903.1 link	n.757+12998C>G	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.333

AC:

50573

AN:

151912

Hom.:

9206

Cov.:

show subpopulations

Gnomad AFR

AF:

0.212

Gnomad AMI

AF:

0.288

Gnomad AMR

AF:

0.443

Gnomad ASJ

AF:

0.280

Gnomad EAS

AF:

0.101

Gnomad SAS

AF:

0.278

Gnomad FIN

AF:

0.433

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.392

Gnomad OTH

AF:

0.302

GnomAD4 exome

AF:

0.353

AC:

AN:

204

Hom.:

Cov.:

AF XY:

0.409

AC XY:

AN XY:

110

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.357

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.214

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.372

AC:

AN:

164

Other (OTH)

AF:

0.167

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.526

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:

0.333

AC:

50589

AN:

152030

Hom.:

9217

Cov.:

AF XY:

0.334

AC XY:

24837

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.212

AC:

8783

AN:

41460

American (AMR)

AF:

0.444

AC:

6773

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.280

AC:

973

AN:

3472

East Asian (EAS)

AF:

0.101

AC:

520

AN:

5164

South Asian (SAS)

AF:

0.279

AC:

1344

AN:

4820

European-Finnish (FIN)

AF:

0.433

AC:

4567

AN:

10550

Middle Eastern (MID)

AF:

0.241

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.392

AC:

26666

AN:

67976

Other (OTH)

AF:

0.298

AC:

629

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1657

3315

4972

6630

8287

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

500

1000

1500

2000

2500

<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:

0.350

Hom.:

1206

Bravo

AF:

0.329

Asia WGS

AF:

0.195

AC:

683

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.34

(source)

DANN

Benign

0.49

PhyloP100

-0.74

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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