11-122120283-T-C

Position:

• chr11-122120283-T-C

Variant summary

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

The ENST00000534782.4(MIR100HG):​n.388-28564A>G 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 0.239 in 152,058 control chromosomes in the GnomAD database, including 4,755 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 0.24 (4755 hom., cov: 32)
• Consequence: MIR100HG ENST00000534782.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR100HG	NR_024430.2	n.492-28543A>G		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137179.1	n.446-28543A>G		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137180.1	n.504-28543A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000534782.4	n.388-28564A>G		intron_variant, non_coding_transcript_variant		1
MIR100HG	ENST00000534297.2	n.186-3960A>G		intron_variant, non_coding_transcript_variant		4
MIR100HG	ENST00000637700.1	n.682-28564A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36334 AN: 151940 Hom.: 4757 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.239 AC: 36343 AN: 152058 Hom.: 4755 Cov.: 32 AF XY: 0.242 AC XY: 18018 AN XY: 74314

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.255

Alfa AF: 0.250 Hom.: 5017

Bravo AF: 0.255

Asia WGS AF: 0.314 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7119477; hg19: chr11-121990991;