11-122190700-C-G

Variant names:

• chr11-122190700-C-G
• rs1971734
• ENST00000527474.5:n.899-10302G>C

Variant summary

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

The ENST00000527474.5(MIR100HG):​n.899-10302G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 151,770 control chromosomes in the GnomAD database, including 4,038 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 0.23 (4038 hom., cov: 32)
• Consequence: MIR100HG ENST00000527474.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 2 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR100HG	NR_024430.2	n.347-10302G>C		intron_variant	Intron 1 of 3
MIR100HG	NR_137179.1	n.301-10302G>C		intron_variant	Intron 2 of 4
MIR100HG	NR_137180.1	n.359-10302G>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000527474.5	n.899-10302G>C		intron_variant	Intron 3 of 3	1
MIR100HG	ENST00000534782.4	n.325-10302G>C		intron_variant	Intron 1 of 2	1
MIR100HG	ENST00000532350.6	n.325-10302G>C		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34302 AN: 151652 Hom.: 4033 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.226 AC: 34310 AN: 151770 Hom.: 4038 Cov.: 32 AF XY: 0.228 AC XY: 16911 AN XY: 74182

African (AFR) AF: 0.165 AC: 6821 AN: 41416

American (AMR) AF: 0.193 AC: 2942 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1101 AN: 3462

East Asian (EAS) AF: 0.268 AC: 1381 AN: 5146

South Asian (SAS) AF: 0.240 AC: 1150 AN: 4796

European-Finnish (FIN) AF: 0.310 AC: 3255 AN: 10510

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16920 AN: 67894

Other (OTH) AF: 0.249 AC: 524 AN: 2108

Alfa AF: 0.137 Hom.: 290

Bravo AF: 0.217

Asia WGS AF: 0.248 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.41
DANN	Benign	0.41
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1971734; hg19: chr11-122061408;