rs41318019

Variant names:

• chr1-207797034-C-G
• rs41318019
• ENST00000710901.1:n.662+8971G>C

Variant summary

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

The ENST00000710901.1(MIR29B2CHG):​n.662+8971G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0656 in 152,146 control chromosomes in the GnomAD database, including 363 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 0.066 (363 hom., cov: 30)
• Consequence: MIR29B2CHG ENST00000710901.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 3 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0885 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	ENST00000710901.1		n.662+8971G>C		intron	N/A
	MIR29B2CHG	ENST00000710902.1		n.569+18895G>C		intron	N/A
	MIR29B2CHG	ENST00000710903.1		n.757+18895G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0657 AC: 9981 AN: 152028 Hom.: 362 Cov.: 30

Gnomad AFR AF: 0.0912

Gnomad AMI AF: 0.0176

Gnomad AMR AF: 0.0422

Gnomad ASJ AF: 0.0237

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0441

Gnomad FIN AF: 0.0483

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0678

Gnomad OTH AF: 0.0522

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

GnomAD4 genome AF: 0.0656 AC: 9985 AN: 152146 Hom.: 363 Cov.: 30 AF XY: 0.0626 AC XY: 4653 AN XY: 74378

African (AFR) AF: 0.0910 AC: 3775 AN: 41498

American (AMR) AF: 0.0422 AC: 645 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0237 AC: 82 AN: 3466

East Asian (EAS) AF: 0.00290 AC: 15 AN: 5174

South Asian (SAS) AF: 0.0443 AC: 214 AN: 4826

European-Finnish (FIN) AF: 0.0483 AC: 511 AN: 10590

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0678 AC: 4610 AN: 67982

Other (OTH) AF: 0.0516 AC: 109 AN: 2112

Alfa AF: 0.0665 Hom.: 42

Bravo AF: 0.0651

Asia WGS AF: 0.0290 AC: 100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.80
DANN	Benign	0.71
PhyloP100		-0.053

Splicing

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

Other links and lift over

dbSNP: rs41318019; hg19: chr1-207970379;