chr11-122147842-T-C

Variant names:

• chr11-122147842-T-C
• rs562052
• ENST00000534782.4:n.387+32494A>G

Variant summary

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

The ENST00000534782.4(MIR100HG):​n.387+32494A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 151,864 control chromosomes in the GnomAD database, including 34,844 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 0.68 (34844 hom., cov: 29)
• Consequence: MIR100HG ENST00000534782.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 5 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000534782.4. 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_024430.2		n.491+7709A>G		intron	N/A
	MIR100HG	NR_137179.1		n.445+7709A>G		intron	N/A
	MIR100HG	NR_137180.1		n.503+7709A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR100HG	ENST00000534782.4	TSL:1	n.387+32494A>G		intron	N/A
	MIR100HG	ENST00000534297.2	TSL:4	n.185+7709A>G		intron	N/A
	MIR100HG	ENST00000637700.1	TSL:5	n.681+7709A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102600 AN: 151744 Hom.: 34806 Cov.: 29

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.657

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.676 AC: 102691 AN: 151864 Hom.: 34844 Cov.: 29 AF XY: 0.678 AC XY: 50307 AN XY: 74224

African (AFR) AF: 0.638 AC: 26370 AN: 41358

American (AMR) AF: 0.724 AC: 11038 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2289 AN: 3470

East Asian (EAS) AF: 0.653 AC: 3365 AN: 5152

South Asian (SAS) AF: 0.558 AC: 2680 AN: 4806

European-Finnish (FIN) AF: 0.760 AC: 8027 AN: 10568

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.685 AC: 46569 AN: 67960

Other (OTH) AF: 0.680 AC: 1430 AN: 2102

Alfa AF: 0.681 Hom.: 4394

Bravo AF: 0.676

Asia WGS AF: 0.615 AC: 2136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.14
DANN	Benign	0.47
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs562052; hg19: chr11-122018550;