11-122081440-A-T

Position:

• chr11-122081440-A-T

Variant summary

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

The ENST00000532319.2(MIR100HG):​n.120-15006T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 152,074 control chromosomes in the GnomAD database, including 40,007 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 0.72 (40007 hom., cov: 32)
• Consequence: MIR100HG ENST00000532319.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113

Genes affected

MIR100HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR100HG	NR_137178.1	n.474-15006T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000530955.2	n.256+20007T>A		intron_variant		5
MIR100HG	ENST00000532319.2	n.120-15006T>A		intron_variant		4
MIR100HG	ENST00000636654.1	n.76-15006T>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.724 AC: 110047 AN: 151956 Hom.: 39979 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.724 AC: 110127 AN: 152074 Hom.: 40007 Cov.: 32 AF XY: 0.723 AC XY: 53723 AN XY: 74346

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.721

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.749

Alfa AF: 0.721 Hom.: 4947

Bravo AF: 0.725

Asia WGS AF: 0.646 AC: 2246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs487330; hg19: chr11-121952148;