2-12063147-G-A

Variant names:

• chr2-12063147-G-A
• rs10495588
• ENST00000412294.6:n.207+55304G>A

Variant summary

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

The ENST00000412294.6(MIR3681HG):​n.207+55304G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,088 control chromosomes in the GnomAD database, including 5,572 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 0.27 (5572 hom., cov: 32)
• Consequence: MIR3681HG ENST00000412294.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786
• Publications: 3 publications found

Genes affected

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

ENSG00000307254 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 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.209+55304G>A		intron	N/A
	MIR3681HG	NR_110197.1		n.210-43671G>A		intron	N/A
	MIR3681HG	NR_110198.1		n.210-20302G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3681HG	ENST00000412294.6	TSL:2	n.207+55304G>A		intron	N/A
	MIR3681HG	ENST00000438292.5	TSL:3	n.128+55304G>A		intron	N/A
	MIR3681HG	ENST00000449986.3	TSL:2	n.198-43309G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40391 AN: 151970 Hom.: 5573 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.266 AC: 40399 AN: 152088 Hom.: 5572 Cov.: 32 AF XY: 0.264 AC XY: 19632 AN XY: 74344

African (AFR) AF: 0.335 AC: 13908 AN: 41456

American (AMR) AF: 0.237 AC: 3621 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 732 AN: 3472

East Asian (EAS) AF: 0.116 AC: 603 AN: 5178

South Asian (SAS) AF: 0.251 AC: 1210 AN: 4812

European-Finnish (FIN) AF: 0.248 AC: 2614 AN: 10556

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16873 AN: 68012

Other (OTH) AF: 0.243 AC: 512 AN: 2106

Alfa AF: 0.261 Hom.: 1767

Bravo AF: 0.265

Asia WGS AF: 0.199 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.034
DANN	Benign	0.36
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs10495588; hg19: chr2-12203273;