11-122148303-A-G

Variant names:

• chr11-122148303-A-G
• rs693120
• ENST00000534782.4:n.387+32033T>C

Variant summary

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

The ENST00000534782.4(MIR100HG):​n.387+32033T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 150,944 control chromosomes in the GnomAD database, including 34,545 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 (34545 hom., cov: 28)
• Consequence: MIR100HG ENST00000534782.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.692
• Publications: 4 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.712 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+7248T>C		intron	N/A
	MIR100HG	NR_137179.1		n.445+7248T>C		intron	N/A
	MIR100HG	NR_137180.1		n.503+7248T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR100HG	ENST00000534782.4	TSL:1	n.387+32033T>C		intron	N/A
	MIR100HG	ENST00000534297.2	TSL:4	n.185+7248T>C		intron	N/A
	MIR100HG	ENST00000637700.1	TSL:5	n.681+7248T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.675 AC: 101807 AN: 150830 Hom.: 34508 Cov.: 28

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.675 AC: 101893 AN: 150944 Hom.: 34545 Cov.: 28 AF XY: 0.676 AC XY: 49796 AN XY: 73622

African (AFR) AF: 0.636 AC: 26173 AN: 41170

American (AMR) AF: 0.724 AC: 10967 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2285 AN: 3462

East Asian (EAS) AF: 0.652 AC: 3346 AN: 5130

South Asian (SAS) AF: 0.556 AC: 2657 AN: 4776

European-Finnish (FIN) AF: 0.756 AC: 7655 AN: 10122

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46464 AN: 67822

Other (OTH) AF: 0.678 AC: 1422 AN: 2098

Alfa AF: 0.672 Hom.: 3619

Asia WGS AF: 0.615 AC: 2137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.6
DANN	Benign	0.75
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs693120; hg19: chr11-122019011; COSMIC: COSV62996596;