rs12410786

Positions:

• chr1-207802860-T-A

Variant summary

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

The NR_135298.1(MIR29B2CHG):​n.922-198A>T 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 0.296 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 NR_135298.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

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=-0.75).
• 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/exons	MANE	Protein	UniProt
MIR29B2CHG	NR_135298.1	n.922-198A>T		intron_variant, non_coding_transcript_variant
MIR29B2CHG	NR_135299.1	n.1107-198A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR29B2CHG	ENST00000710901.1	n.662+3145A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44100 AN: 152026 Hom.: 6925 Cov.: 32

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.: 0 AF XY: 0.467 AC XY: 1452 AN XY: 3108

Gnomad4 AFR exome AF: 0.330

Gnomad4 AMR exome AF: 0.599

Gnomad4 ASJ exome AF: 0.331

Gnomad4 EAS exome AF: 0.225

Gnomad4 SAS exome AF: 0.372

Gnomad4 FIN exome AF: 0.539

Gnomad4 NFE exome AF: 0.491

Gnomad4 OTH exome AF: 0.484

GnomAD4 genome AF: 0.290 AC: 44116 AN: 152142 Hom.: 6938 Cov.: 32 AF XY: 0.293 AC XY: 21803 AN XY: 74380

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.0982

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.260

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
DANN	Benign	0.84

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12410786; hg19: chr1-207976205;