rs512932

Positions:

• chr11-122102833-A-G

Variant summary

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

The ENST00000534782.4(MIR100HG):​n.388-11114T>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 0.184 in 151,612 control chromosomes in the GnomAD database, including 2,696 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 0.18 (2696 hom., cov: 31)
• Consequence: MIR100HG ENST00000534782.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22

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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR100HG	NR_024430.2	n.492-11093T>C		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137179.1	n.446-11093T>C		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137180.1	n.504-11093T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR100HG	ENST00000534782.4	n.388-11114T>C		intron_variant, non_coding_transcript_variant		1
MIR100HG	ENST00000532315.1	n.872+2238T>C		intron_variant, non_coding_transcript_variant		4
MIR100HG	ENST00000534195.1	n.99+2238T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27871 AN: 151494 Hom.: 2699 Cov.: 31

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.184 AC: 27876 AN: 151612 Hom.: 2696 Cov.: 31 AF XY: 0.185 AC XY: 13719 AN XY: 74066

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.173

Alfa AF: 0.201 Hom.: 3334

Bravo AF: 0.178

Asia WGS AF: 0.269 AC: 939 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.9
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs512932; hg19: chr11-121973541;