rs2084637

Variant names:

• chr11-122520479-T-C
• rs2084637
• ENST00000533109.6:n.433+19000A>G

Variant summary

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

The ENST00000533109.6(MIR100HG):​n.433+19000A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,116 control chromosomes in the GnomAD database, including 6,659 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 (6659 hom., cov: 32)
• Consequence: MIR100HG ENST00000533109.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108

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=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000533109.6	n.433+19000A>G		intron_variant	Intron 3 of 6	5

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41668 AN: 151998 Hom.: 6667 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.274 AC: 41656 AN: 152116 Hom.: 6659 Cov.: 32 AF XY: 0.275 AC XY: 20460 AN XY: 74336

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.270

Alfa AF: 0.334 Hom.: 17476

Bravo AF: 0.251

Asia WGS AF: 0.352 AC: 1224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.8
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2084637; hg19: chr11-122391187;