rs947893

chr11-122091791-A-Gchr11-122091791-A-T

Variant summary

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

The NR_137178.1(MIR100HG):n.473+8583T>C 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 0.343 in 152,018 control chromosomes in the GnomAD database, including 8,932 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 0.34 (8931 hom., cov: 32)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: MIR100HG NR_137178.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284

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=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR100HG	NR_137178.1	n.473+8583T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR100HG	ENST00000524376.2	n.76-72T>C		intron_variant, non_coding_transcript_variant		1
MIR100HG	ENST00000528986.2	n.897-51T>C		intron_variant, non_coding_transcript_variant		1
MIR100HG	ENST00000534782.4	n.388-72T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52110 AN: 151896 Hom.: 8925 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.359

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 0.750

GnomAD4 genome AF: 0.343 AC: 52149 AN: 152014 Hom.: 8931 Cov.: 32 AF XY: 0.340 AC XY: 25281 AN XY: 74314

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.355

Alfa AF: 0.360 Hom.: 1233

Bravo AF: 0.344

Asia WGS AF: 0.329 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	13
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs947893; hg19: chr11-121962499;