chr2-12428870-G-A

Variant names:

• chr2-12428870-G-A
• rs10929808
• ENST00000412294.6:n.422+120086G>A

Variant summary

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

The ENST00000412294.6(MIR3681HG):​n.422+120086G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.86 in 152,236 control chromosomes in the GnomAD database, including 56,690 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 0.86 (56690 hom., cov: 33)
• Consequence: MIR3681HG ENST00000412294.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213
• Publications: 10 publications found

Genes affected

MIR3681HG (HGNC:52001): (MIR3681 host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412294.6. 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
	MIR3681HG	NR_110196.1		n.424+120086G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3681HG	ENST00000412294.6	TSL:2	n.422+120086G>A		intron	N/A
	MIR3681HG	ENST00000412606.2	TSL:5	n.85+114465G>A		intron	N/A
	MIR3681HG	ENST00000653212.1		n.437+12584G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.859 AC: 130725 AN: 152118 Hom.: 56634 Cov.: 33

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.860 AC: 130849 AN: 152236 Hom.: 56690 Cov.: 33 AF XY: 0.852 AC XY: 63422 AN XY: 74428

African (AFR) AF: 0.899 AC: 37337 AN: 41538

American (AMR) AF: 0.830 AC: 12710 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 3004 AN: 3470

East Asian (EAS) AF: 0.533 AC: 2753 AN: 5162

South Asian (SAS) AF: 0.630 AC: 3033 AN: 4816

European-Finnish (FIN) AF: 0.902 AC: 9570 AN: 10604

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.876 AC: 59620 AN: 68026

Other (OTH) AF: 0.870 AC: 1835 AN: 2108

Alfa AF: 0.864 Hom.: 178232

Bravo AF: 0.859

Asia WGS AF: 0.601 AC: 2093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.25
PhyloP100		0.21

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: rs10929808;

hg19: chr2-12568996;