rs1318653

Variant names:

• chr1-207841577-T-C
• rs1318653
• ENST00000608023.6:n.222-22431A>G

Variant summary

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

The ENST00000608023.6(MIR29B2CHG):​n.222-22431A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 146,818 control chromosomes in the GnomAD database, including 2,908 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 (2908 hom., cov: 28)
• Consequence: MIR29B2CHG ENST00000608023.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367

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=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.231 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	ENST00000608023.6	n.222-22431A>G		intron_variant	Intron 2 of 4	5
MIR29B2CHG	ENST00000637970.1	n.590-24163A>G		intron_variant	Intron 4 of 7	5
MIR29B2CHG	ENST00000710901.1	n.242-24163A>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.193 AC: 28283 AN: 146772 Hom.: 2904 Cov.: 28

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.00593

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.173

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.166

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.193 AC: 28282 AN: 146818 Hom.: 2908 Cov.: 28 AF XY: 0.191 AC XY: 13650 AN XY: 71346

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.00575

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.165

Alfa AF: 0.205 Hom.: 407

Bravo AF: 0.195

Asia WGS AF: 0.0800 AC: 280 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.2
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1318653; hg19: chr1-208014922;