ENST00000657366.1:n.405T>C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ENSG00000308093 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000435542.4	n.242+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

GnomAD2 exomes AF: 0.0871 AC: 19920 AN: 228648 AF XY: 0.0870

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 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

African (AFR) AF: 0.210 AC: 2208 AN: 10502

American (AMR) AF: 0.0664 AC: 2408 AN: 36268

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 2049 AN: 11720

East Asian (EAS) AF: 0.000228 AC: 3 AN: 13172

South Asian (SAS) AF: 0.0672 AC: 4480 AN: 66624

European-Finnish (FIN) AF: 0.0677 AC: 1145 AN: 16908

Middle Eastern (MID) AF: 0.178 AC: 508 AN: 2852

European-Non Finnish (NFE) AF: 0.0883 AC: 16929 AN: 191690

Other (OTH) AF: 0.0946 AC: 1570 AN: 16604

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

African (AFR) AF: 0.210 AC: 8721 AN: 41538

American (AMR) AF: 0.0989 AC: 1513 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3470

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.0634 AC: 306 AN: 4830

European-Finnish (FIN) AF: 0.0652 AC: 692 AN: 10612

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.0891 AC: 6063 AN: 68024

Other (OTH) AF: 0.137 AC: 290 AN: 2116

Alfa AF: 0.109 Hom.: 360

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
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs17009221; hg19: chr1-208050301;