rs17009221

Variant names:

• chr1-207876956-A-G
• rs17009221
• ENST00000657366.1:n.405T>C

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR29B2CHG	ENST00000657366.1	n.405T>C		non_coding_transcript_exon_variant	Exon 3 of 5
MIR29B2CHG	ENST00000435542.3	n.202+1924T>C		intron_variant	Intron 1 of 2	3
MIR29B2CHG	ENST00000637970.1	n.217+1924T>C		intron_variant	Intron 1 of 7	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;