2-12112224-A-G

Variant names:

• chr2-12112224-A-G
• rs17551536
• ENST00000412294.6:n.208-54514A>G

Variant summary

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

The ENST00000412294.6(MIR3681HG):​n.208-54514A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,148 control chromosomes in the GnomAD database, including 3,234 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 0.20 (3234 hom., cov: 32)
• Consequence: MIR3681HG ENST00000412294.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 6 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR3681HG	NR_110196.1	n.210-54514A>G		intron_variant	Intron 2 of 5
MIR3681HG	NR_110197.1	n.343+5273A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3681HG	ENST00000412294.6	n.208-54514A>G		intron_variant	Intron 2 of 5	2
MIR3681HG	ENST00000438292.5	n.129-54514A>G		intron_variant	Intron 2 of 4	3
MIR3681HG	ENST00000449986.3	n.560+5273A>G		intron_variant	Intron 4 of 4	2

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29719 AN: 152030 Hom.: 3214 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.00886

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.196 AC: 29775 AN: 152148 Hom.: 3234 Cov.: 32 AF XY: 0.192 AC XY: 14266 AN XY: 74382

African (AFR) AF: 0.269 AC: 11148 AN: 41478

American (AMR) AF: 0.146 AC: 2230 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 732 AN: 3470

East Asian (EAS) AF: 0.00888 AC: 46 AN: 5182

South Asian (SAS) AF: 0.208 AC: 1001 AN: 4812

European-Finnish (FIN) AF: 0.133 AC: 1413 AN: 10604

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12646 AN: 67994

Other (OTH) AF: 0.180 AC: 380 AN: 2114

Alfa AF: 0.184 Hom.: 7727

Bravo AF: 0.197

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.14
DANN	Benign	0.55
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs17551536; hg19: chr2-12252350;