11-122120283-T-C

Variant names:

• chr11-122120283-T-C
• rs7119477
• ENST00000534782.4:n.388-28564A>G

Variant summary

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

The ENST00000534782.4(MIR100HG):​n.388-28564A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,058 control chromosomes in the GnomAD database, including 4,755 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 0.24 (4755 hom., cov: 32)
• Consequence: MIR100HG ENST00000534782.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR100HG	NR_024430.2	n.492-28543A>G		intron_variant	Intron 3 of 3
MIR100HG	NR_137179.1	n.446-28543A>G		intron_variant	Intron 4 of 4
MIR100HG	NR_137180.1	n.504-28543A>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000534782.4	n.388-28564A>G		intron_variant	Intron 2 of 2	1
MIR100HG	ENST00000534297.2	n.186-3960A>G		intron_variant	Intron 2 of 3	4
MIR100HG	ENST00000637700.1	n.682-28564A>G		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36334 AN: 151940 Hom.: 4757 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.239 AC: 36343 AN: 152058 Hom.: 4755 Cov.: 32 AF XY: 0.242 AC XY: 18018 AN XY: 74314

African (AFR) AF: 0.165 AC: 6833 AN: 41470

American (AMR) AF: 0.394 AC: 6019 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 820 AN: 3470

East Asian (EAS) AF: 0.345 AC: 1775 AN: 5152

South Asian (SAS) AF: 0.268 AC: 1289 AN: 4818

European-Finnish (FIN) AF: 0.216 AC: 2282 AN: 10572

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16401 AN: 67980

Other (OTH) AF: 0.255 AC: 537 AN: 2108

Alfa AF: 0.251 Hom.: 6453

Bravo AF: 0.255

Asia WGS AF: 0.314 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.18
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7119477; hg19: chr11-121990991;