11-122190700-C-G

Position:

• chr11-122190700-C-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

MIR100HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
MIR100HG	NR_024430.2	n.347-10302G>C		intron_variant
MIR100HG	NR_137179.1	n.301-10302G>C		intron_variant
MIR100HG	NR_137180.1	n.359-10302G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000527474.5	n.899-10302G>C		intron_variant		1
MIR100HG	ENST00000534782.4	n.325-10302G>C		intron_variant		1
MIR100HG	ENST00000532350.6	n.325-10302G>C		intron_variant		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

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.249

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1971734; hg19: chr11-122061408;