chr11-122161260-C-G

Variant names:

• chr11-122161260-C-G
• rs12273515
• ENST00000534782.4:n.387+19076G>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+19076G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,082 control chromosomes in the GnomAD database, including 5,629 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 0.27 (5629 hom., cov: 33)
• Consequence: MIR100HG ENST00000534782.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR100HG	NR_024430.2	n.410-5628G>C		intron_variant	Intron 2 of 3
MIR100HG	NR_137179.1	n.364-5628G>C		intron_variant	Intron 3 of 4
MIR100HG	NR_137180.1	n.422-5628G>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000534782.4	n.387+19076G>C		intron_variant	Intron 2 of 2	1
MIR100HG	ENST00000532350.6	n.388-5628G>C		intron_variant	Intron 2 of 2	5
MIR100HG	ENST00000533109.6	n.917-5628G>C		intron_variant	Intron 6 of 6	5

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40584 AN: 151964 Hom.: 5615 Cov.: 33

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.267 AC: 40642 AN: 152082 Hom.: 5629 Cov.: 33 AF XY: 0.272 AC XY: 20228 AN XY: 74334

African (AFR) AF: 0.293 AC: 12158 AN: 41490

American (AMR) AF: 0.366 AC: 5592 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 660 AN: 3470

East Asian (EAS) AF: 0.409 AC: 2109 AN: 5152

South Asian (SAS) AF: 0.274 AC: 1321 AN: 4818

European-Finnish (FIN) AF: 0.235 AC: 2488 AN: 10578

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15456 AN: 67982

Other (OTH) AF: 0.251 AC: 531 AN: 2112

Alfa AF: 0.251 Hom.: 588

Bravo AF: 0.278

Asia WGS AF: 0.332 AC: 1154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.49
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs12273515; hg19: chr11-122031968;