ENST00000524376.2:n.76-72T>C

Variant names:

• chr11-122091791-A-G
• rs947893
• ENST00000524376.3:n.129-72T>C

Variant summary

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

The ENST00000524376.3(MIR100HG):​n.129-72T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 152,018 control chromosomes in the GnomAD database, including 8,932 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 0.34 (8931 hom., cov: 32)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: MIR100HG ENST00000524376.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.359 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.492-51T>C		intron	N/A
	MIR100HG	NR_137175.1		n.784-72T>C		intron	N/A
	MIR100HG	NR_137176.1		n.474-51T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR100HG	ENST00000524376.3	TSL:1	n.129-72T>C		intron	N/A
	MIR100HG	ENST00000528986.2	TSL:1	n.897-51T>C		intron	N/A
	MIR100HG	ENST00000534782.4	TSL:1	n.388-72T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52110 AN: 151896 Hom.: 8925 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.359

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.750 AC: 3 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.343 AC: 52149 AN: 152014 Hom.: 8931 Cov.: 32 AF XY: 0.340 AC XY: 25281 AN XY: 74314

African (AFR) AF: 0.326 AC: 13542 AN: 41482

American (AMR) AF: 0.321 AC: 4892 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 958 AN: 3464

East Asian (EAS) AF: 0.321 AC: 1662 AN: 5176

South Asian (SAS) AF: 0.355 AC: 1713 AN: 4820

European-Finnish (FIN) AF: 0.340 AC: 3599 AN: 10580

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24624 AN: 67922

Other (OTH) AF: 0.355 AC: 747 AN: 2106

Alfa AF: 0.359 Hom.: 1274

Bravo AF: 0.344

Asia WGS AF: 0.329 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	13
DANN	Benign	0.82
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs947893; hg19: chr11-121962499;