chr11-122168344-T-G

Variant names:

• chr11-122168344-T-G
• rs11218544
• ENST00000534782.4:n.387+11992A>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+11992A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,070 control chromosomes in the GnomAD database, including 2,079 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 0.16 (2079 hom., cov: 32)
• Consequence: MIR100HG ENST00000534782.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 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.409+11992A>C		intron	N/A
	MIR100HG	NR_137179.1		n.363+11992A>C		intron	N/A
	MIR100HG	NR_137180.1		n.421+11992A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR100HG	ENST00000534782.4	TSL:1	n.387+11992A>C		intron	N/A
	MIR100HG	ENST00000532350.6	TSL:5	n.387+11992A>C		intron	N/A
	MIR100HG	ENST00000533109.6	TSL:5	n.916+11992A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23647 AN: 151950 Hom.: 2073 Cov.: 32

Gnomad AFR AF: 0.0796

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.156 AC: 23663 AN: 152070 Hom.: 2079 Cov.: 32 AF XY: 0.160 AC XY: 11891 AN XY: 74326

African (AFR) AF: 0.0793 AC: 3296 AN: 41542

American (AMR) AF: 0.187 AC: 2860 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 583 AN: 3470

East Asian (EAS) AF: 0.377 AC: 1942 AN: 5148

South Asian (SAS) AF: 0.218 AC: 1050 AN: 4814

European-Finnish (FIN) AF: 0.166 AC: 1752 AN: 10586

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11591 AN: 67930

Other (OTH) AF: 0.164 AC: 346 AN: 2114

Alfa AF: 0.164 Hom.: 1646

Bravo AF: 0.152

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.71
DANN	Benign	0.48
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs11218544; hg19: chr11-122039052;