chr1-207841577-T-C

Variant names:

• chr1-207841577-T-C
• rs1318653
• ENST00000608023.7:n.222-22431A>G

Variant summary

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

The ENST00000710901.1(MIR29B2CHG):​n.242-24163A>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 ENST00000710901.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367
• Publications: 20 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=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000710901.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR29B2CHG	ENST00000608023.7	TSL:5	n.222-22431A>G		intron	N/A
	MIR29B2CHG	ENST00000637970.1	TSL:5	n.590-24163A>G		intron	N/A
	MIR29B2CHG	ENST00000710901.1		n.242-24163A>G		intron	N/A

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

African (AFR) AF: 0.180 AC: 7118 AN: 39598

American (AMR) AF: 0.238 AC: 3509 AN: 14772

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 481 AN: 3458

East Asian (EAS) AF: 0.00575 AC: 29 AN: 5046

South Asian (SAS) AF: 0.145 AC: 674 AN: 4664

European-Finnish (FIN) AF: 0.207 AC: 1858 AN: 8974

Middle Eastern (MID) AF: 0.165 AC: 47 AN: 284

European-Non Finnish (NFE) AF: 0.211 AC: 14133 AN: 67106

Other (OTH) AF: 0.165 AC: 331 AN: 2010

Alfa AF: 0.205 Hom.: 4416

Bravo AF: 0.195

Asia WGS AF: 0.0800 AC: 280 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.2
DANN	Benign	0.88
PhyloP100		-0.37

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1318653;

hg19: chr1-208014922;