rs56075814

Positions:

• chr1-207802604-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428

Genes affected

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

ACMG classification

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	n.980A>G		non_coding_transcript_exon_variant	5/5
MIR29B2CHG	NR_135299.1	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	n.662+3401A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29646 AN: 151980 Hom.: 3072 Cov.: 32

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.: 0 AF XY: 0.196 AC XY: 35043 AN XY: 178514

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.: 32 AF XY: 0.193 AC XY: 14382 AN XY: 74362

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

Other links and lift over

dbSNP: rs56075814; hg19: chr1-207975949; COSMIC: COSV66080695;