11-122173583-C-G

Position:

• chr11-122173583-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000534782.4(MIR100HG):​n.387+6753G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,902 control chromosomes in the GnomAD database, including 8,493 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 0.32 (8493 hom., cov: 32)
• Consequence: MIR100HG ENST00000534782.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.738

Genes affected

MIR100HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR100HG	NR_024430.2	n.409+6753G>C		intron_variant
MIR100HG	NR_137179.1	n.363+6753G>C		intron_variant
MIR100HG	NR_137180.1	n.421+6753G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000534782.4	n.387+6753G>C		intron_variant		1
MIR100HG	ENST00000532350.6	n.387+6753G>C		intron_variant		5
MIR100HG	ENST00000533109.6	n.916+6753G>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48604 AN: 151784 Hom.: 8495 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.320 AC: 48599 AN: 151902 Hom.: 8493 Cov.: 32 AF XY: 0.324 AC XY: 24016 AN XY: 74234

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.359

Alfa AF: 0.207 Hom.: 484

Bravo AF: 0.305

Asia WGS AF: 0.440 AC: 1528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.3
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1615327; hg19: chr11-122044291;