rs664409

Variant names:

• chr11-122093861-G-A
• rs664409
• ENST00000524376.3:n.129-2142C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000524376.3(MIR100HG):​n.129-2142C>T variant causes a intron 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 ENST00000524376.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.407
• Publications: 6 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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000524376.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR100HG	NR_024430.2		n.492-2121C>T		intron	N/A
	MIR100HG	NR_137175.1		n.784-2142C>T		intron	N/A
	MIR100HG	NR_137176.1		n.474-2121C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR100HG	ENST00000524376.3	TSL:1	n.129-2142C>T		intron	N/A
	MIR100HG	ENST00000528986.2	TSL:1	n.897-2121C>T		intron	N/A
	MIR100HG	ENST00000534782.4	TSL:1	n.388-2142C>T		intron	N/A

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

African (AFR) AF: 0.331 AC: 13719 AN: 41424

American (AMR) AF: 0.433 AC: 6613 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1533 AN: 3468

East Asian (EAS) AF: 0.317 AC: 1641 AN: 5170

South Asian (SAS) AF: 0.313 AC: 1506 AN: 4810

European-Finnish (FIN) AF: 0.421 AC: 4438 AN: 10540

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.370 AC: 25111 AN: 67942

Other (OTH) AF: 0.385 AC: 809 AN: 2104

Alfa AF: 0.371 Hom.: 30445

Bravo AF: 0.365

Asia WGS AF: 0.292 AC: 1017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.41
DANN	Benign	0.33
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs664409; hg19: chr11-121964569;