Variant 1-207802931-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_135298.1(MIR29B2CHG):n.922-269C>G variant causes a intron, non coding transcript 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
NR_135298.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.742

Variant links:

Genes affected

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

MIR29B2CHG links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
MIR29B2CHG	NR_135298.1 linkuse as main transcript	n.922-269C>G		intron_variant, non_coding_transcript_variant
MIR29B2CHG	NR_135299.1 linkuse as main transcript	n.1107-269C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR29B2CHG	ENST00000710901.1 linkuse as main transcript	n.662+3074C>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AMR exome

AF:

0.357

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.214

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.372

Gnomad4 OTH exome

AF:

0.167

GnomAD4 genome

AF:

0.333

AC:

50589

AN:

152030

Hom.:

9217

Cov.:

AF XY:

0.334

AC XY:

24837

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.212

Gnomad4 AMR

AF:

0.444

Gnomad4 ASJ

AF:

0.280

Gnomad4 EAS

AF:

0.101

Gnomad4 SAS

AF:

0.279

Gnomad4 FIN

AF:

0.433

Gnomad4 NFE

AF:

0.392

Gnomad4 OTH

AF:

0.298

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

DANN

Benign

0.49

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over