11-122147842-T-C

Position:

• chr11-122147842-T-C

Variant summary

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

The ENST00000534782.4(MIR100HG):​n.387+32494A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 151,864 control chromosomes in the GnomAD database, including 34,844 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 0.68 (34844 hom., cov: 29)
• Consequence: MIR100HG ENST00000534782.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

Genes affected

MIR100HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR100HG	NR_024430.2	n.491+7709A>G		intron_variant
MIR100HG	NR_137179.1	n.445+7709A>G		intron_variant
MIR100HG	NR_137180.1	n.503+7709A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000534782.4	n.387+32494A>G		intron_variant		1
MIR100HG	ENST00000534297.2	n.185+7709A>G		intron_variant		4
MIR100HG	ENST00000637700.1	n.681+7709A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102600 AN: 151744 Hom.: 34806 Cov.: 29

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.657

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.676 AC: 102691 AN: 151864 Hom.: 34844 Cov.: 29 AF XY: 0.678 AC XY: 50307 AN XY: 74224

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.680

Alfa AF: 0.681 Hom.: 4394

Bravo AF: 0.676

Asia WGS AF: 0.615 AC: 2136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.14
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs562052; hg19: chr11-122018550;