rs11604461

Positions:

• chr11-122163292-T-C

Variant summary

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

The ENST00000533109.6(MIR100HG):​n.917-7660A>G 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 0.0985 in 152,062 control chromosomes in the GnomAD database, including 971 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 0.099 (971 hom., cov: 32)
• Consequence: MIR100HG ENST00000533109.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156

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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR100HG	NR_024430.2	n.410-7660A>G		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137179.1	n.364-7660A>G		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137180.1	n.422-7660A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR100HG	ENST00000533109.6	n.917-7660A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0987 AC: 14995 AN: 151944 Hom.: 974 Cov.: 32

Gnomad AFR AF: 0.0245

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0964

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.0985 AC: 14980 AN: 152062 Hom.: 971 Cov.: 32 AF XY: 0.0977 AC XY: 7263 AN XY: 74316

Gnomad4 AFR AF: 0.0244

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0964

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.132

Alfa AF: 0.123 Hom.: 1231

Bravo AF: 0.0969

Asia WGS AF: 0.163 AC: 565 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11604461; hg19: chr11-122034000;