18-39294538-A-G

Variant names:

• chr18-39294538-A-G
• rs7233056
• ENST00000591469.1:n.334+33228T>C

Variant summary

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

The ENST00000591469.1(MIR924HG):​n.334+33228T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.864 in 152,140 control chromosomes in the GnomAD database, including 57,108 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 0.86 (57108 hom., cov: 31)
• Consequence: MIR924HG ENST00000591469.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 1 publications found

Genes affected

MIR924HG (HGNC:44332): (MIR924 host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000591469.1. 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
	MIR924HG	NR_024391.1		n.282-85749T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR924HG	ENST00000591469.1	TSL:1	n.334+33228T>C		intron	N/A
	MIR924HG	ENST00000591629.2	TSL:2	n.441-85749T>C		intron	N/A
	MIR924HG	ENST00000652839.1		n.428-18740T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.864 AC: 131373 AN: 152022 Hom.: 57058 Cov.: 31

Gnomad AFR AF: 0.952

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.852

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.864 AC: 131479 AN: 152140 Hom.: 57108 Cov.: 31 AF XY: 0.867 AC XY: 64494 AN XY: 74358

African (AFR) AF: 0.951 AC: 39506 AN: 41522

American (AMR) AF: 0.871 AC: 13318 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.852 AC: 2955 AN: 3470

East Asian (EAS) AF: 0.847 AC: 4370 AN: 5160

South Asian (SAS) AF: 0.887 AC: 4277 AN: 4824

European-Finnish (FIN) AF: 0.877 AC: 9274 AN: 10576

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.811 AC: 55159 AN: 67984

Other (OTH) AF: 0.842 AC: 1781 AN: 2114

Alfa AF: 0.853 Hom.: 9365

Bravo AF: 0.866

Asia WGS AF: 0.866 AC: 3010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.27
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs7233056; hg19: chr18-36874502;