2-12059092-T-C

Variant names:

• chr2-12059092-T-C
• rs7562854
• ENST00000412294.6:n.207+51249T>C

Variant summary

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

The ENST00000412294.6(MIR3681HG):​n.207+51249T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 152,164 control chromosomes in the GnomAD database, including 43,936 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 0.76 (43936 hom., cov: 32)
• Consequence: MIR3681HG ENST00000412294.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.903
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR3681HG	NR_110196.1	n.209+51249T>C		intron_variant	Intron 2 of 5
MIR3681HG	NR_110197.1	n.210-47726T>C		intron_variant	Intron 2 of 3
MIR3681HG	NR_110198.1	n.210-24357T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3681HG	ENST00000412294.6	n.207+51249T>C		intron_variant	Intron 2 of 5	2
MIR3681HG	ENST00000438292.5	n.128+51249T>C		intron_variant	Intron 2 of 4	3
MIR3681HG	ENST00000449986.3	n.198-47364T>C		intron_variant	Intron 2 of 4	2

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115243 AN: 152046 Hom.: 43878 Cov.: 32

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.758 AC: 115360 AN: 152164 Hom.: 43936 Cov.: 32 AF XY: 0.760 AC XY: 56579 AN XY: 74408

African (AFR) AF: 0.707 AC: 29322 AN: 41498

American (AMR) AF: 0.824 AC: 12593 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2682 AN: 3468

East Asian (EAS) AF: 0.871 AC: 4520 AN: 5188

South Asian (SAS) AF: 0.833 AC: 4019 AN: 4822

European-Finnish (FIN) AF: 0.722 AC: 7638 AN: 10578

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.765 AC: 52024 AN: 68006

Other (OTH) AF: 0.777 AC: 1644 AN: 2116

Alfa AF: 0.750 Hom.: 8386

Bravo AF: 0.762

Asia WGS AF: 0.867 AC: 3016 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.15
DANN	Benign	0.78
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs7562854; hg19: chr2-12199218;