18-39356146-T-C

Variant names:

• chr18-39356146-T-C
• rs993979
• ENST00000591629.2:n.441-147357A>G

Variant summary

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

The ENST00000591629.2(MIR924HG):​n.441-147357A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.695 in 152,010 control chromosomes in the GnomAD database, including 36,895 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 0.69 (36895 hom., cov: 31)
• Consequence: MIR924HG ENST00000591629.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR924HG	NR_024391.1	n.282-147357A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR924HG	ENST00000591629.2	n.441-147357A>G		intron_variant	Intron 3 of 3	2
MIR924HG	ENST00000652839.1	n.428-80348A>G		intron_variant	Intron 3 of 3
MIR924HG	ENST00000652860.2	n.536-28195A>G		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105497 AN: 151892 Hom.: 36849 Cov.: 31

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.695 AC: 105597 AN: 152010 Hom.: 36895 Cov.: 31 AF XY: 0.697 AC XY: 51786 AN XY: 74286

African (AFR) AF: 0.722 AC: 29921 AN: 41434

American (AMR) AF: 0.682 AC: 10419 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2221 AN: 3472

East Asian (EAS) AF: 0.731 AC: 3760 AN: 5144

South Asian (SAS) AF: 0.743 AC: 3581 AN: 4818

European-Finnish (FIN) AF: 0.740 AC: 7816 AN: 10560

Middle Eastern (MID) AF: 0.733 AC: 214 AN: 292

European-Non Finnish (NFE) AF: 0.671 AC: 45598 AN: 67996

Other (OTH) AF: 0.698 AC: 1474 AN: 2112

Alfa AF: 0.677 Hom.: 58249

Bravo AF: 0.694

Asia WGS AF: 0.770 AC: 2674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.36
DANN	Benign	0.36
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs993979; hg19: chr18-36936110;