chr1-207851475-C-T

Position:

• chr1-207851475-C-T

Variant summary

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

The ENST00000710901.1(MIR29B2CHG):​n.241+16451G>A variant causes a intron, non coding transcript 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 ENST00000710901.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

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=-0.84).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR29B2CHG	ENST00000710901.1	n.241+16451G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0203

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.0905

Gnomad4 SAS AF: 0.0865

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.0908

Alfa AF: 0.104 Hom.: 1657

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12731740; hg19: chr1-208024820;