11-122155230-C-G

Variant names:

• chr11-122155230-C-G
• rs638742
• ENST00000534782.4:n.387+25106G>C

Variant summary

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

The ENST00000532350.6(MIR100HG):​n.790G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,998 control chromosomes in the GnomAD database, including 14,148 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 0.40 (14148 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: MIR100HG ENST00000532350.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR100HG	NR_024430.2	n.491+321G>C		intron_variant	Intron 3 of 3
MIR100HG	NR_137179.1	n.445+321G>C		intron_variant	Intron 4 of 4
MIR100HG	NR_137180.1	n.503+321G>C		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000534782.4	n.387+25106G>C		intron_variant	Intron 2 of 2	1
MIR100HG	ENST00000532350.6	n.790G>C		non_coding_transcript_exon_variant	Exon 3 of 3	5
MIR100HG	ENST00000533109.6	n.1319G>C		non_coding_transcript_exon_variant	Exon 7 of 7	5

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60573 AN: 151882 Hom.: 14143 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.411

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.399 AC: 60582 AN: 151998 Hom.: 14148 Cov.: 32 AF XY: 0.404 AC XY: 29977 AN XY: 74268

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.411

Alfa AF: 0.455 Hom.: 2155

Bravo AF: 0.367

Asia WGS AF: 0.367 AC: 1275 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.8
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs638742; hg19: chr11-122025938;