11-122081440-A-T

Variant names:

• chr11-122081440-A-T
• rs487330
• ENST00000530955.3:n.682+20007T>A

Variant summary

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

The ENST00000532319.2(MIR100HG):​n.120-15006T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 152,074 control chromosomes in the GnomAD database, including 40,007 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 0.72 (40007 hom., cov: 32)
• Consequence: MIR100HG ENST00000532319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000532319.2. 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
	MIR100HG	NR_137178.1		n.474-15006T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR100HG	ENST00000530955.3	TSL:5	n.682+20007T>A		intron	N/A
	MIR100HG	ENST00000532319.2	TSL:4	n.120-15006T>A		intron	N/A
	MIR100HG	ENST00000636654.1	TSL:5	n.76-15006T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.724 AC: 110047 AN: 151956 Hom.: 39979 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.724 AC: 110127 AN: 152074 Hom.: 40007 Cov.: 32 AF XY: 0.723 AC XY: 53723 AN XY: 74346

African (AFR) AF: 0.704 AC: 29202 AN: 41470

American (AMR) AF: 0.757 AC: 11562 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.721 AC: 2505 AN: 3472

East Asian (EAS) AF: 0.638 AC: 3303 AN: 5174

South Asian (SAS) AF: 0.680 AC: 3275 AN: 4816

European-Finnish (FIN) AF: 0.759 AC: 8033 AN: 10578

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.732 AC: 49772 AN: 67972

Other (OTH) AF: 0.749 AC: 1583 AN: 2114

Alfa AF: 0.721 Hom.: 4947

Bravo AF: 0.725

Asia WGS AF: 0.646 AC: 2246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.60
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs487330; hg19: chr11-121952148;