rs17009221

chr1-207876956-A-G

Variant summary

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

The ENST00000657366.1(MIR29B2CHG):n.405T>C 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 0.0956 in 518,622 control chromosomes in the GnomAD database, including 2,964 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 0.12 (1340 hom., cov: 33)
  • Exomes 𝑓: 0.085 (1624 hom.)
• Consequence: MIR29B2CHG ENST00000657366.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR29B2CHG	ENST00000657366.1	n.405T>C		non_coding_transcript_exon_variant	3/5
MIR29B2CHG	ENST00000435542.3	n.202+1924T>C		intron_variant, non_coding_transcript_variant		3
MIR29B2CHG	ENST00000637970.1	n.217+1924T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18244 AN: 152164 Hom.: 1336 Cov.: 33

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0990

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0631

Gnomad FIN AF: 0.0652

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0891

Gnomad OTH AF: 0.138

GnomAD3 exomes AF: 0.0871 AC: 19920 AN: 228648 Hom.: 1153 AF XY: 0.0870 AC XY: 10996 AN XY: 126372

Gnomad AFR exome AF: 0.212

Gnomad AMR exome AF: 0.0660

Gnomad ASJ exome AF: 0.177

Gnomad EAS exome AF: 0.000114

Gnomad SAS exome AF: 0.0650

Gnomad FIN exome AF: 0.0669

Gnomad NFE exome AF: 0.0912

Gnomad OTH exome AF: 0.107

GnomAD4 exome AF: 0.0854 AC: 31300 AN: 366340 Hom.: 1624 Cov.: 0 AF XY: 0.0849 AC XY: 17832 AN XY: 210020

Gnomad4 AFR exome AF: 0.210

Gnomad4 AMR exome AF: 0.0664

Gnomad4 ASJ exome AF: 0.175

Gnomad4 EAS exome AF: 0.000228

Gnomad4 SAS exome AF: 0.0672

Gnomad4 FIN exome AF: 0.0677

Gnomad4 NFE exome AF: 0.0883

Gnomad4 OTH exome AF: 0.0946

GnomAD4 genome AF: 0.120 AC: 18258 AN: 152282 Hom.: 1340 Cov.: 33 AF XY: 0.116 AC XY: 8643 AN XY: 74462

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.0989

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0634

Gnomad4 FIN AF: 0.0652

Gnomad4 NFE AF: 0.0891

Gnomad4 OTH AF: 0.137

Alfa AF: 0.112 Hom.: 246

Bravo AF: 0.126

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.4
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17009221; hg19: chr1-208050301;