rs1967689

Variant names:

• chr1-207866126-G-C
• rs1967689
• ENST00000608023.7:n.221+1800C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000608023.7(MIR29B2CHG):​n.221+1800C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,006 control chromosomes in the GnomAD database, including 3,013 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 (3013 hom., cov: 31)
• Consequence: MIR29B2CHG ENST00000608023.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150
• Publications: 15 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.236 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	ENST00000608023.7	n.221+1800C>G		intron_variant	Intron 2 of 8	5
MIR29B2CHG	ENST00000637970.1	n.589+1800C>G		intron_variant	Intron 4 of 7	5
MIR29B2CHG	ENST00000710901.1	n.241+1800C>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28704 AN: 151888 Hom.: 3007 Cov.: 31

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.00464

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.189 AC: 28715 AN: 152006 Hom.: 3013 Cov.: 31 AF XY: 0.188 AC XY: 13953 AN XY: 74302

African (AFR) AF: 0.125 AC: 5201 AN: 41452

American (AMR) AF: 0.242 AC: 3694 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3468

East Asian (EAS) AF: 0.00446 AC: 23 AN: 5162

South Asian (SAS) AF: 0.142 AC: 685 AN: 4814

European-Finnish (FIN) AF: 0.218 AC: 2306 AN: 10562

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15703 AN: 67968

Other (OTH) AF: 0.168 AC: 355 AN: 2112

Alfa AF: 0.207 Hom.: 404

Bravo AF: 0.190

Asia WGS AF: 0.0810 AC: 282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.6
DANN	Benign	0.60
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1967689; hg19: chr1-208039471;