18-39333908-C-T

Position:

• chr18-39333908-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

MIR924HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
MIR924HG	NR_024391.1	n.282-125119G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR924HG	ENST00000591469.1	n.149-5957G>A		intron_variant		1
MIR924HG	ENST00000591629.2	n.441-125119G>A		intron_variant		2
MIR924HG	ENST00000652839.1	n.428-58110G>A		intron_variant

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

Gnomad4 AFR AF: 0.919

Gnomad4 AMR AF: 0.837

Gnomad4 ASJ AF: 0.840

Gnomad4 EAS AF: 0.966

Gnomad4 SAS AF: 0.942

Gnomad4 FIN AF: 0.929

Gnomad4 NFE AF: 0.855

Gnomad4 OTH AF: 0.877

Alfa AF: 0.848 Hom.: 2359

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1469593; hg19: chr18-36913872;