18-39333908-C-T

Variant names:

• chr18-39333908-C-T
• rs1469593
• ENST00000591469.1:n.149-5957G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000591469.1(MIR924HG):​n.149-5957G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.882 in 152,076 control chromosomes in the GnomAD database, including 59,335 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 0.88 (59335 hom., cov: 31)
• Consequence: MIR924HG ENST00000591469.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR924HG	NR_024391.1	n.282-125119G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR924HG	ENST00000591469.1	n.149-5957G>A		intron_variant	Intron 1 of 3	1
MIR924HG	ENST00000591629.2	n.441-125119G>A		intron_variant	Intron 3 of 3	2
MIR924HG	ENST00000652839.1	n.428-58110G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.882 AC: 134064 AN: 151958 Hom.: 59270 Cov.: 31

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.942

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.882 AC: 134189 AN: 152076 Hom.: 59335 Cov.: 31 AF XY: 0.887 AC XY: 65922 AN XY: 74338

African (AFR) AF: 0.919 AC: 38153 AN: 41510

American (AMR) AF: 0.837 AC: 12788 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.840 AC: 2913 AN: 3466

East Asian (EAS) AF: 0.966 AC: 4993 AN: 5168

South Asian (SAS) AF: 0.942 AC: 4539 AN: 4816

European-Finnish (FIN) AF: 0.929 AC: 9830 AN: 10576

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.855 AC: 58120 AN: 67946

Other (OTH) AF: 0.877 AC: 1853 AN: 2114

Alfa AF: 0.856 Hom.: 2691

Bravo AF: 0.877

Asia WGS AF: 0.949 AC: 3300 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	13
DANN	Benign	0.69
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1469593; hg19: chr18-36913872;