ENST00000511703.7:n.388+2490G>A

Variant names:

• chr4-184848005-C-T
• rs2046813
• ENST00000511703.7:n.388+2490G>A

Variant summary

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

The ENST00000511703.7(MIR3945HG):​n.388+2490G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 151,886 control chromosomes in the GnomAD database, including 27,758 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 0.59 (27758 hom., cov: 31)
• Consequence: MIR3945HG ENST00000511703.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 11 publications found

Genes affected

MIR3945HG (HGNC:52002): (MIR3945 host gene)

ENSG00000286256 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR3945HG	NR_132989.1	n.289+2490G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3945HG	ENST00000511703.7	n.388+2490G>A		intron_variant	Intron 2 of 2	1
MIR3945HG	ENST00000510284.2	n.323-1471G>A		intron_variant	Intron 2 of 2	4
ENSG00000286256	ENST00000651765.1	n.1036-2376C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90153 AN: 151768 Hom.: 27760 Cov.: 31

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.594 AC: 90184 AN: 151886 Hom.: 27758 Cov.: 31 AF XY: 0.593 AC XY: 44055 AN XY: 74238

African (AFR) AF: 0.436 AC: 18038 AN: 41384

American (AMR) AF: 0.619 AC: 9450 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2167 AN: 3466

East Asian (EAS) AF: 0.451 AC: 2329 AN: 5164

South Asian (SAS) AF: 0.603 AC: 2906 AN: 4822

European-Finnish (FIN) AF: 0.689 AC: 7252 AN: 10528

Middle Eastern (MID) AF: 0.606 AC: 177 AN: 292

European-Non Finnish (NFE) AF: 0.677 AC: 46006 AN: 67936

Other (OTH) AF: 0.594 AC: 1253 AN: 2108

Alfa AF: 0.639 Hom.: 8994

Bravo AF: 0.578

Asia WGS AF: 0.499 AC: 1733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.7
DANN	Benign	0.31
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2046813; hg19: chr4-185769159;