11-122173583-C-G

Variant names:

• chr11-122173583-C-G
• rs1615327
• ENST00000534782.4:n.387+6753G>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+6753G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,902 control chromosomes in the GnomAD database, including 8,493 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 0.32 (8493 hom., cov: 32)
• Consequence: MIR100HG ENST00000534782.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.738
• 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 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.409+6753G>C		intron	N/A
	MIR100HG	NR_137179.1		n.363+6753G>C		intron	N/A
	MIR100HG	NR_137180.1		n.421+6753G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR100HG	ENST00000534782.4	TSL:1	n.387+6753G>C		intron	N/A
	MIR100HG	ENST00000532350.6	TSL:5	n.387+6753G>C		intron	N/A
	MIR100HG	ENST00000533109.6	TSL:5	n.916+6753G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48604 AN: 151784 Hom.: 8495 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.320 AC: 48599 AN: 151902 Hom.: 8493 Cov.: 32 AF XY: 0.324 AC XY: 24016 AN XY: 74234

African (AFR) AF: 0.178 AC: 7384 AN: 41438

American (AMR) AF: 0.285 AC: 4356 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1375 AN: 3472

East Asian (EAS) AF: 0.497 AC: 2555 AN: 5144

South Asian (SAS) AF: 0.364 AC: 1753 AN: 4820

European-Finnish (FIN) AF: 0.431 AC: 4551 AN: 10560

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25527 AN: 67888

Other (OTH) AF: 0.359 AC: 757 AN: 2110

Alfa AF: 0.207 Hom.: 484

Bravo AF: 0.305

Asia WGS AF: 0.440 AC: 1528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.3
DANN	Benign	0.70
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs1615327; hg19: chr11-122044291;