4-184846787-C-T

Variant names:

• chr4-184846787-C-T
• rs12641551
• ENST00000511703.7:n.389-1862G>A

Variant summary

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

The ENST00000511703.7(MIR3945HG):​n.389-1862G>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 151,832 control chromosomes in the GnomAD database, including 27,736 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 (27736 hom., cov: 30)
• Consequence: MIR3945HG ENST00000511703.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.785
• Publications: 3 publications found

Genes affected

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

ENSG00000286256 (HGNC:58916):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000511703.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3945HG	NR_132989.1		n.290-1862G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3945HG	ENST00000511703.7	TSL:1	n.389-1862G>A		intron	N/A
	MIR3945HG	ENST00000510284.2	TSL:4	n.323-253G>A		intron	N/A
	ENSG00000286256	ENST00000651765.1		n.1035+2319C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90084 AN: 151714 Hom.: 27738 Cov.: 30

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.604

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: 90116 AN: 151832 Hom.: 27736 Cov.: 30 AF XY: 0.593 AC XY: 44025 AN XY: 74214

African (AFR) AF: 0.435 AC: 18006 AN: 41374

American (AMR) AF: 0.617 AC: 9418 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2164 AN: 3462

East Asian (EAS) AF: 0.452 AC: 2333 AN: 5162

South Asian (SAS) AF: 0.604 AC: 2914 AN: 4822

European-Finnish (FIN) AF: 0.689 AC: 7265 AN: 10546

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 45977 AN: 67892

Other (OTH) AF: 0.594 AC: 1254 AN: 2110

Alfa AF: 0.639 Hom.: 58946

Bravo AF: 0.578

Asia WGS AF: 0.499 AC: 1733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	14
DANN	Benign	0.75
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs12641551; hg19: chr4-185767941;