rs2046813

Positions:

• chr4-184848005-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_132989.1(MIR3945HG):​n.289+2490G>A variant causes a intron, non coding transcript 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 NR_132989.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
MIR3945HG	NR_132989.1	n.289+2490G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3945HG	ENST00000511703.7	n.388+2490G>A		intron_variant, non_coding_transcript_variant		1
	ENST00000656863.1	n.674-2376C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.594

Alfa AF: 0.624 Hom.: 5106

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2046813; hg19: chr4-185769159;