2-12072319-A-G

Variant names:

• chr2-12072319-A-G
• rs16858228
• ENST00000412294.6:n.207+64476A>G

Variant summary

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

The ENST00000412294.6(MIR3681HG):​n.207+64476A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0314 in 152,342 control chromosomes in the GnomAD database, including 156 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 0.031 (156 hom., cov: 32)
• Consequence: MIR3681HG ENST00000412294.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 5 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0912 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.209+64476A>G		intron	N/A
	MIR3681HG	NR_110197.1		n.210-34499A>G		intron	N/A
	MIR3681HG	NR_110198.1		n.210-11130A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3681HG	ENST00000412294.6	TSL:2	n.207+64476A>G		intron	N/A
	MIR3681HG	ENST00000438292.5	TSL:3	n.128+64476A>G		intron	N/A
	MIR3681HG	ENST00000449986.3	TSL:2	n.198-34137A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0314 AC: 4775 AN: 152224 Hom.: 156 Cov.: 32

Gnomad AFR AF: 0.00774

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0950

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.0583

Gnomad SAS AF: 0.0707

Gnomad FIN AF: 0.0217

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0291

Gnomad OTH AF: 0.0363

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

GnomAD4 genome AF: 0.0314 AC: 4779 AN: 152342 Hom.: 156 Cov.: 32 AF XY: 0.0333 AC XY: 2478 AN XY: 74506

African (AFR) AF: 0.00772 AC: 321 AN: 41588

American (AMR) AF: 0.0952 AC: 1458 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 42 AN: 3472

East Asian (EAS) AF: 0.0584 AC: 303 AN: 5186

South Asian (SAS) AF: 0.0708 AC: 342 AN: 4830

European-Finnish (FIN) AF: 0.0217 AC: 230 AN: 10616

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0291 AC: 1981 AN: 68020

Other (OTH) AF: 0.0359 AC: 76 AN: 2116

Alfa AF: 0.0317 Hom.: 346

Bravo AF: 0.0361

Asia WGS AF: 0.0540 AC: 187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.57
PhyloP100		-0.13

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: rs16858228;

hg19: chr2-12212445;