11-122107043-G-C

Variant names:

• chr11-122107043-G-C
• rs10790486
• ENST00000534782.4:n.388-15324C>G

Variant summary

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

The ENST00000534782.4(MIR100HG):​n.388-15324C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 152,018 control chromosomes in the GnomAD database, including 23,746 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 0.55 (23746 hom., cov: 32)
• Consequence: MIR100HG ENST00000534782.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240
• 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]

ENSG00000301769 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.614 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR100HG	NR_024430.2		n.492-15303C>G		intron	N/A
	MIR100HG	NR_137179.1		n.446-15303C>G		intron	N/A
	MIR100HG	NR_137180.1		n.504-15303C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR100HG	ENST00000534782.4	TSL:1	n.388-15324C>G		intron	N/A
	ENSG00000301769	ENST00000781641.1		n.113G>C		non_coding_transcript_exon	Exon 2 of 6
	MIR100HG	ENST00000534297.2	TSL:4	n.376+9090C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83488 AN: 151900 Hom.: 23736 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.549 AC: 83532 AN: 152018 Hom.: 23746 Cov.: 32 AF XY: 0.552 AC XY: 41022 AN XY: 74314

African (AFR) AF: 0.410 AC: 16974 AN: 41424

American (AMR) AF: 0.496 AC: 7574 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1828 AN: 3472

East Asian (EAS) AF: 0.586 AC: 3025 AN: 5164

South Asian (SAS) AF: 0.572 AC: 2755 AN: 4820

European-Finnish (FIN) AF: 0.712 AC: 7531 AN: 10582

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 42060 AN: 67960

Other (OTH) AF: 0.546 AC: 1152 AN: 2110

Alfa AF: 0.476 Hom.: 1501

Bravo AF: 0.524

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.7
DANN	Benign	0.81
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs10790486; hg19: chr11-121977751;