chr11-122081440-A-T

Variant names:

• chr11-122081440-A-T
• rs487330
• ENST00000530955.2:n.256+20007T>A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR100HG	NR_137178.1	n.474-15006T>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000530955.2	n.256+20007T>A		intron_variant	Intron 1 of 1	5
MIR100HG	ENST00000532319.2	n.120-15006T>A		intron_variant	Intron 1 of 3	4
MIR100HG	ENST00000636654.1	n.76-15006T>A		intron_variant	Intron 1 of 7	5

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

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.721

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.749

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs487330; hg19: chr11-121952148;