ENST00000534782.4:n.387+24584G>A

Variant names:

• chr11-122155752-C-T
• rs1816158
• ENST00000534782.4:n.387+24584G>A

Variant summary

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

The ENST00000534782.4(MIR100HG):​n.387+24584G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 (52595 hom., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: MIR100HG ENST00000534782.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 7 publications found

Genes affected

MIR100HG (HGNC:39522): (mir-100-let-7a-2-mir-125b-1 cluster host gene) This gene produces long non-coding RNAs that act as regulators of cell proliferation. Alternative promoter usage and splicing results in multiple transcript variants. Some transcript variants may promote growth, while others may act to negatively regulate cell division. [provided by RefSeq, May 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR100HG	NR_024430.2	n.410-120G>A		intron_variant	Intron 2 of 3
MIR100HG	NR_137179.1	n.364-120G>A		intron_variant	Intron 3 of 4
MIR100HG	NR_137180.1	n.422-120G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000534782.4	n.387+24584G>A		intron_variant	Intron 2 of 2	1
MIR100HG	ENST00000780507.1	n.549G>A		non_coding_transcript_exon_variant	Exon 1 of 1
MIR100HG	ENST00000532350.6	n.388-120G>A		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.855 AC: 122602 AN: 143420 Hom.: 52554 Cov.: 20

Gnomad AFR AF: 0.867

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.859

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.855 AC: 122680 AN: 143484 Hom.: 52595 Cov.: 20 AF XY: 0.854 AC XY: 59027 AN XY: 69114

African (AFR) AF: 0.867 AC: 33611 AN: 38748

American (AMR) AF: 0.884 AC: 12661 AN: 14326

Ashkenazi Jewish (ASJ) AF: 0.827 AC: 2845 AN: 3442

East Asian (EAS) AF: 0.629 AC: 3000 AN: 4766

South Asian (SAS) AF: 0.718 AC: 3182 AN: 4430

European-Finnish (FIN) AF: 0.918 AC: 7161 AN: 7800

Middle Eastern (MID) AF: 0.868 AC: 243 AN: 280

European-Non Finnish (NFE) AF: 0.860 AC: 57436 AN: 66806

Other (OTH) AF: 0.858 AC: 1698 AN: 1980

Alfa AF: 0.857 Hom.: 12622

Bravo AF: 0.851

Asia WGS AF: 0.654 AC: 2261 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.6
DANN	Benign	0.52
PhyloP100		0.056

Splicing

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

Other links and lift over

dbSNP: rs1816158; hg19: chr11-122026460;