rs577948

Variant names:

• chr11-122159482-A-G
• rs577948
• ENST00000534782.4:n.387+20854T>C

Variant summary

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

The ENST00000534782.4(MIR100HG):​n.387+20854T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,092 control chromosomes in the GnomAD database, including 9,506 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 (9506 hom., cov: 32)
• Consequence: MIR100HG ENST00000534782.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496
• Publications: 33 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 (EAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000534782.4. 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_024430.2		n.410-3850T>C		intron	N/A
	MIR100HG	NR_137179.1		n.364-3850T>C		intron	N/A
	MIR100HG	NR_137180.1		n.422-3850T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR100HG	ENST00000534782.4	TSL:1	n.387+20854T>C		intron	N/A
	MIR100HG	ENST00000532350.6	TSL:5	n.388-3850T>C		intron	N/A
	MIR100HG	ENST00000533109.6	TSL:5	n.917-3850T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51507 AN: 151974 Hom.: 9498 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.339 AC: 51525 AN: 152092 Hom.: 9506 Cov.: 32 AF XY: 0.343 AC XY: 25497 AN XY: 74324

African (AFR) AF: 0.172 AC: 7131 AN: 41516

American (AMR) AF: 0.352 AC: 5376 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1450 AN: 3470

East Asian (EAS) AF: 0.511 AC: 2631 AN: 5152

South Asian (SAS) AF: 0.399 AC: 1923 AN: 4820

European-Finnish (FIN) AF: 0.443 AC: 4689 AN: 10576

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27045 AN: 67962

Other (OTH) AF: 0.373 AC: 787 AN: 2110

Alfa AF: 0.384 Hom.: 50854

Bravo AF: 0.328

Asia WGS AF: 0.473 AC: 1644 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	9.4
DANN	Benign	0.88
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs577948; hg19: chr11-122030190;