Variant 1-207802604-T-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.980A>G 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 0.2 in 469,686 control chromosomes in the GnomAD database, including 10,319 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 0.19 ( 3079 hom., cov: 32)

Exomes 𝑓: 0.20 ( 7240 hom. )

Consequence

MIR29B2CHG
NR_135298.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.428

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=-0.81).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.235 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.980A>G		non_coding_transcript_exon_variant	5/5
MIR29B2CHG	NR_135299.1 linkuse as main transcript	n.1165A>G		non_coding_transcript_exon_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR29B2CHG	ENST00000710901.1 linkuse as main transcript	n.662+3401A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.195

AC:

29646

AN:

151980

Hom.:

3072

Cov.:

show subpopulations

Gnomad AFR

AF:

0.176

Gnomad AMI

AF:

0.113

Gnomad AMR

AF:

0.241

Gnomad ASJ

AF:

0.140

Gnomad EAS

AF:

0.00617

Gnomad SAS

AF:

0.143

Gnomad FIN

AF:

0.221

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.215

Gnomad OTH

AF:

0.171

GnomAD4 exome

AF:

0.202

AC:

64090

AN:

317588

Hom.:

7240

Cov.:

AF XY:

0.196

AC XY:

35043

AN XY:

178514

show subpopulations

Gnomad4 AFR exome

AF:

0.174

Gnomad4 AMR exome

AF:

0.301

Gnomad4 ASJ exome

AF:

0.130

Gnomad4 EAS exome

AF:

0.00599

Gnomad4 SAS exome

AF:

0.163

Gnomad4 FIN exome

AF:

0.217

Gnomad4 NFE exome

AF:

0.218

Gnomad4 OTH exome

AF:

0.187

GnomAD4 genome

AF:

0.195

AC:

29655

AN:

152098

Hom.:

3079

Cov.:

AF XY:

0.193

AC XY:

14382

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.176

Gnomad4 AMR

AF:

0.242

Gnomad4 ASJ

AF:

0.140

Gnomad4 EAS

AF:

0.00599

Gnomad4 SAS

AF:

0.142

Gnomad4 FIN

AF:

0.221

Gnomad4 NFE

AF:

0.215

Gnomad4 OTH

AF:

0.169

Alfa

AF:

0.202

Hom.:

378

Bravo

AF:

0.197

Asia WGS

AF:

0.0790

AC:

278

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

9.0

DANN

Benign

0.81

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