11-122168344-T-G

Variant summary

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

The ENST00000533109.6(MIR100HG):n.916+11992A>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 0.156 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 ENST00000533109.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR100HG	NR_024430.2	n.409+11992A>C		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137179.1	n.363+11992A>C		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137180.1	n.421+11992A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR100HG	ENST00000533109.6	n.916+11992A>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.0793

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.164

Alfa AF: 0.157 Hom.: 1046

Bravo AF: 0.152

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.71
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11218544; hg19: chr11-122039052;