rs664409

Positions:

• chr11-122093861-G-A
• chr11-122093861-G-C

Variant summary

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

The NR_137178.1(MIR100HG):​n.473+6513C>T 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 0.367 in 151,928 control chromosomes in the GnomAD database, including 10,346 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 0.37 (10346 hom., cov: 32)
• Consequence: MIR100HG NR_137178.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.407

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 (AMR) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR100HG	NR_137178.1	n.473+6513C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR100HG	ENST00000524376.2	n.76-2142C>T		intron_variant, non_coding_transcript_variant		1
MIR100HG	ENST00000528986.2	n.897-2121C>T		intron_variant, non_coding_transcript_variant		1
MIR100HG	ENST00000534782.4	n.388-2142C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55807 AN: 151808 Hom.: 10345 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.367 AC: 55824 AN: 151928 Hom.: 10346 Cov.: 32 AF XY: 0.369 AC XY: 27398 AN XY: 74264

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.385

Alfa AF: 0.373 Hom.: 18909

Bravo AF: 0.365

Asia WGS AF: 0.292 AC: 1017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.41
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs664409; hg19: chr11-121964569;