11-122418564-A-G

Position:

• chr11-122418564-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000533109.6(MIR100HG):​n.433+120915T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 151,606 control chromosomes in the GnomAD database, including 4,781 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 0.24 (4781 hom., cov: 31)
• Consequence: MIR100HG ENST00000533109.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR100HG	NR_137179.1	n.180+4128T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000533109.6	n.433+120915T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37111 AN: 151488 Hom.: 4771 Cov.: 31

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.245 AC: 37143 AN: 151606 Hom.: 4781 Cov.: 31 AF XY: 0.245 AC XY: 18145 AN XY: 74040

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.229

Alfa AF: 0.247 Hom.: 685

Bravo AF: 0.248

Asia WGS AF: 0.299 AC: 1037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	2.5
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs559453; hg19: chr11-122289272;