ENST00000654302.1:n.242-5859C>G

Variant names:

• chr18-5737301-C-G
• rs1880722
• ENST00000654302.1:n.242-5859C>G

Variant summary

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

The ENST00000654302.1(MIR3976HG):​n.242-5859C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,174 control chromosomes in the GnomAD database, including 1,942 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 0.11 (1942 hom., cov: 33)
• Consequence: MIR3976HG ENST00000654302.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257
• Publications: 0 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 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.242-5859C>G		intron	N/A
	MIR3976HG	ENST00000656406.1		n.896+2694C>G		intron	N/A
	MIR3976HG	ENST00000661123.1		n.911-1062C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16202 AN: 152054 Hom.: 1934 Cov.: 33

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0948

Gnomad ASJ AF: 0.0576

Gnomad EAS AF: 0.0529

Gnomad SAS AF: 0.0347

Gnomad FIN AF: 0.0219

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0243

Gnomad OTH AF: 0.0931

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

GnomAD4 genome AF: 0.107 AC: 16248 AN: 152174 Hom.: 1942 Cov.: 33 AF XY: 0.104 AC XY: 7758 AN XY: 74396

African (AFR) AF: 0.291 AC: 12052 AN: 41464

American (AMR) AF: 0.0950 AC: 1452 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0576 AC: 200 AN: 3470

East Asian (EAS) AF: 0.0529 AC: 274 AN: 5184

South Asian (SAS) AF: 0.0345 AC: 166 AN: 4810

European-Finnish (FIN) AF: 0.0219 AC: 232 AN: 10614

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0243 AC: 1651 AN: 68024

Other (OTH) AF: 0.0926 AC: 196 AN: 2116

Alfa AF: 0.0741 Hom.: 151

Bravo AF: 0.123

Asia WGS AF: 0.0480 AC: 166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.53
DANN	Benign	0.53
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs1880722; hg19: chr18-5737300;