ENST00000654302.1:n.242-953A>G

Variant names:

• chr18-5742207-A-G
• rs4798405
• ENST00000654302.1:n.242-953A>G

Variant summary

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

The ENST00000654302.1(MIR3976HG):​n.242-953A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 152,096 control chromosomes in the GnomAD database, including 30,013 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 0.61 (30013 hom., cov: 33)
• Consequence: MIR3976HG ENST00000654302.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 2 publications found

Genes affected

MIR3976HG (HGNC:51104): (MIR3976 host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654302.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3976HG	ENST00000654302.1		n.242-953A>G		intron	N/A
	MIR3976HG	ENST00000656406.1		n.897-958A>G		intron	N/A
	MIR3976HG	ENST00000661123.1		n.1876-953A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92954 AN: 151978 Hom.: 29951 Cov.: 33

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.612 AC: 93082 AN: 152096 Hom.: 30013 Cov.: 33 AF XY: 0.610 AC XY: 45358 AN XY: 74360

African (AFR) AF: 0.826 AC: 34290 AN: 41504

American (AMR) AF: 0.639 AC: 9765 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1659 AN: 3468

East Asian (EAS) AF: 0.455 AC: 2353 AN: 5170

South Asian (SAS) AF: 0.598 AC: 2887 AN: 4826

European-Finnish (FIN) AF: 0.485 AC: 5127 AN: 10574

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35165 AN: 67958

Other (OTH) AF: 0.573 AC: 1208 AN: 2110

Alfa AF: 0.547 Hom.: 38321

Bravo AF: 0.633

Asia WGS AF: 0.598 AC: 2082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.75
PhyloP100		0.027

Splicing

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

Other links and lift over

dbSNP: rs4798405; hg19: chr18-5742206;