11-122146890-C-T

Position:

• chr11-122146890-C-T

Variant summary

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

The ENST00000534782.4(MIR100HG):​n.387+33446G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 151,752 control chromosomes in the GnomAD database, including 21,894 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 0.53 (21894 hom., cov: 32)
• Consequence: MIR100HG ENST00000534782.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

Genes affected

MIR100HG (HGNC:39522): (mir-100-let-7a-2-mir-125b-1 cluster host gene) This gene produces long non-coding RNAs that act as regulators of cell proliferation. Alternative promoter usage and splicing results in multiple transcript variants. Some transcript variants may promote growth, while others may act to negatively regulate cell division. [provided by RefSeq, May 2016]

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 (NFE) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR100HG	NR_024430.2	n.491+8661G>A		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137179.1	n.445+8661G>A		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137180.1	n.503+8661G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000534782.4	n.387+33446G>A		intron_variant, non_coding_transcript_variant		1
MIR100HG	ENST00000534297.2	n.185+8661G>A		intron_variant, non_coding_transcript_variant		4
MIR100HG	ENST00000637700.1	n.681+8661G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80804 AN: 151634 Hom.: 21883 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.533 AC: 80852 AN: 151752 Hom.: 21894 Cov.: 32 AF XY: 0.532 AC XY: 39459 AN XY: 74170

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.687

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.539

Alfa AF: 0.557 Hom.: 2969

Bravo AF: 0.510

Asia WGS AF: 0.462 AC: 1604 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.4
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1143770; hg19: chr11-122017598;