2-12500615-G-A

Variant names:

• chr2-12500615-G-A
• rs1534422
• ENST00000412294.6:n.423-57591G>A

Variant summary

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

The ENST00000412294.6(MIR3681HG):​n.423-57591G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 151,908 control chromosomes in the GnomAD database, including 20,978 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 0.52 (20978 hom., cov: 31)
• Consequence: MIR3681HG ENST00000412294.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 44 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 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.425-57591G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3681HG	ENST00000412294.6	TSL:2	n.423-57591G>A		intron	N/A
	MIR3681HG	ENST00000412606.2	TSL:5	n.86-57591G>A		intron	N/A
	MIR3681HG	ENST00000653212.1		n.438-57591G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79142 AN: 151790 Hom.: 20965 Cov.: 31

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.521 AC: 79187 AN: 151908 Hom.: 20978 Cov.: 31 AF XY: 0.525 AC XY: 38979 AN XY: 74228

African (AFR) AF: 0.431 AC: 17848 AN: 41416

American (AMR) AF: 0.535 AC: 8170 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1712 AN: 3464

East Asian (EAS) AF: 0.726 AC: 3734 AN: 5146

South Asian (SAS) AF: 0.530 AC: 2548 AN: 4804

European-Finnish (FIN) AF: 0.605 AC: 6377 AN: 10538

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37026 AN: 67962

Other (OTH) AF: 0.546 AC: 1150 AN: 2106

Alfa AF: 0.531 Hom.: 52755

Bravo AF: 0.515

Asia WGS AF: 0.587 AC: 2041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.65
DANN	Benign	0.68
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1534422; hg19: chr2-12640741;