rs12731740

Variant names:

• chr1-207851475-C-T
• rs12731740
• ENST00000608023.7:n.221+16451G>A

Variant summary

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

The ENST00000608023.7(MIR29B2CHG):​n.221+16451G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0916 in 152,160 control chromosomes in the GnomAD database, including 889 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 0.092 (889 hom., cov: 32)
• Consequence: MIR29B2CHG ENST00000608023.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 37 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.16 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+16451G>A		intron_variant	Intron 2 of 8	5
MIR29B2CHG	ENST00000637970.1	n.589+16451G>A		intron_variant	Intron 4 of 7	5
MIR29B2CHG	ENST00000710901.1	n.241+16451G>A		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.0917 AC: 13936 AN: 152042 Hom.: 888 Cov.: 32

Gnomad AFR AF: 0.0204

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0905

Gnomad SAS AF: 0.0860

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.0916 AC: 13943 AN: 152160 Hom.: 889 Cov.: 32 AF XY: 0.0967 AC XY: 7194 AN XY: 74372

African (AFR) AF: 0.0203 AC: 844 AN: 41546

American (AMR) AF: 0.165 AC: 2523 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 401 AN: 3472

East Asian (EAS) AF: 0.0905 AC: 468 AN: 5172

South Asian (SAS) AF: 0.0865 AC: 417 AN: 4822

European-Finnish (FIN) AF: 0.164 AC: 1734 AN: 10558

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7202 AN: 67984

Other (OTH) AF: 0.0908 AC: 192 AN: 2114

Alfa AF: 0.104 Hom.: 3707

Bravo AF: 0.0897

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.1
DANN	Benign	0.59
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs12731740; hg19: chr1-208024820;