rs668183

Variant names:

• chr11-122395997-T-G
• rs668183
• ENST00000526674.2:n.180+26695A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000526674.2(MIR100HG):​n.180+26695A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,032 control chromosomes in the GnomAD database, including 6,460 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 0.28 (6460 hom., cov: 32)
• Consequence: MIR100HG ENST00000526674.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 3 publications found

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]

ENSG00000301744 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000526674.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR100HG	NR_137179.1		n.180+26695A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR100HG	ENST00000526674.2	TSL:5	n.180+26695A>C		intron	N/A
	MIR100HG	ENST00000533109.6	TSL:5	n.434-102391A>C		intron	N/A
	MIR100HG	ENST00000637700.1	TSL:5	n.116+57619A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42429 AN: 151912 Hom.: 6445 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.279 AC: 42486 AN: 152032 Hom.: 6460 Cov.: 32 AF XY: 0.279 AC XY: 20725 AN XY: 74326

African (AFR) AF: 0.397 AC: 16466 AN: 41456

American (AMR) AF: 0.272 AC: 4158 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1016 AN: 3468

East Asian (EAS) AF: 0.316 AC: 1633 AN: 5168

South Asian (SAS) AF: 0.305 AC: 1472 AN: 4820

European-Finnish (FIN) AF: 0.227 AC: 2397 AN: 10568

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14619 AN: 67960

Other (OTH) AF: 0.253 AC: 535 AN: 2114

Alfa AF: 0.265 Hom.: 741

Bravo AF: 0.287

Asia WGS AF: 0.318 AC: 1105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.23
DANN	Benign	0.52
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs668183; hg19: chr11-122266705;