11-122148303-A-G

Position:

• chr11-122148303-A-G

Variant summary

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

The ENST00000534782.4(MIR100HG):​n.387+32033T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 150,944 control chromosomes in the GnomAD database, including 34,545 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 (34545 hom., cov: 28)
• Consequence: MIR100HG ENST00000534782.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.692

Genes affected

MIR100HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR100HG	NR_024430.2	n.491+7248T>C		intron_variant
MIR100HG	NR_137179.1	n.445+7248T>C		intron_variant
MIR100HG	NR_137180.1	n.503+7248T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000534782.4	n.387+32033T>C		intron_variant		1
MIR100HG	ENST00000534297.2	n.185+7248T>C		intron_variant		4
MIR100HG	ENST00000637700.1	n.681+7248T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.675 AC: 101807 AN: 150830 Hom.: 34508 Cov.: 28

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.675 AC: 101893 AN: 150944 Hom.: 34545 Cov.: 28 AF XY: 0.676 AC XY: 49796 AN XY: 73622

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.756

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.678

Alfa AF: 0.672 Hom.: 3619

Asia WGS AF: 0.615 AC: 2137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs693120; hg19: chr11-122019011; COSMIC: COSV62996596;