rs565229

Positions:

• chr11-122318757-G-A
• chr11-122318757-G-T

Variant summary

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

The ENST00000527474.5(MIR100HG):​n.479-25151C>T 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 0.119 in 152,072 control chromosomes in the GnomAD database, including 1,195 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 0.12 (1195 hom., cov: 32)
• Consequence: MIR100HG ENST00000527474.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.657

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR100HG	NR_137179.1	n.181-26354C>T		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137192.1	n.494-26354C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR100HG	ENST00000533109.6	n.434-25151C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18147 AN: 151952 Hom.: 1195 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.0994

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.119 AC: 18167 AN: 152072 Hom.: 1195 Cov.: 32 AF XY: 0.122 AC XY: 9079 AN XY: 74332

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.0993

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.113

Alfa AF: 0.112 Hom.: 1340

Bravo AF: 0.118

Asia WGS AF: 0.182 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs565229; hg19: chr11-122189465;