2-12190273-G-A

Variant names:

• chr2-12190273-G-A
• rs10495594
• ENST00000412294.6:n.325+23418G>A

Variant summary

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

The ENST00000412294.6(MIR3681HG):​n.325+23418G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 151,904 control chromosomes in the GnomAD database, including 1,831 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 0.11 (1831 hom., cov: 31)
• Consequence: MIR3681HG ENST00000412294.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358
• Publications: 2 publications found

Genes affected

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

ENSG00000289856 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3681HG	NR_110196.1		n.327+23418G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3681HG	ENST00000412294.6	TSL:2	n.325+23418G>A		intron	N/A
	MIR3681HG	ENST00000438292.5	TSL:3	n.246+23418G>A		intron	N/A
	ENSG00000289856	ENST00000701120.2		n.416-479C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17158 AN: 151786 Hom.: 1823 Cov.: 31

Gnomad AFR AF: 0.0421

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.0648

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.0807

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0909

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.113 AC: 17191 AN: 151904 Hom.: 1831 Cov.: 31 AF XY: 0.123 AC XY: 9169 AN XY: 74244

African (AFR) AF: 0.0424 AC: 1756 AN: 41448

American (AMR) AF: 0.235 AC: 3579 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0648 AC: 225 AN: 3470

East Asian (EAS) AF: 0.460 AC: 2369 AN: 5152

South Asian (SAS) AF: 0.399 AC: 1918 AN: 4808

European-Finnish (FIN) AF: 0.0807 AC: 851 AN: 10540

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0909 AC: 6176 AN: 67932

Other (OTH) AF: 0.126 AC: 266 AN: 2108

Alfa AF: 0.109 Hom.: 727

Bravo AF: 0.119

Asia WGS AF: 0.418 AC: 1452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.57
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs10495594; hg19: chr2-12330399;