rs17126243

Positions:

• chr11-122178967-G-A
• chr11-122178967-G-C

Variant summary

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

The ENST00000533109.6(MIR100HG):​n.916+1369C>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 0.0851 in 152,164 control chromosomes in the GnomAD database, including 664 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 0.085 (664 hom., cov: 32)
• Consequence: MIR100HG ENST00000533109.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR100HG	NR_024430.2	n.409+1369C>T		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137179.1	n.363+1369C>T		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137180.1	n.421+1369C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR100HG	ENST00000533109.6	n.916+1369C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0851 AC: 12936 AN: 152046 Hom.: 664 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.0104

Gnomad SAS AF: 0.0373

Gnomad FIN AF: 0.0698

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0602

Gnomad OTH AF: 0.0742

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

GnomAD4 genome AF: 0.0851 AC: 12954 AN: 152164 Hom.: 664 Cov.: 32 AF XY: 0.0848 AC XY: 6309 AN XY: 74380

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.0222

Gnomad4 EAS AF: 0.0104

Gnomad4 SAS AF: 0.0373

Gnomad4 FIN AF: 0.0698

Gnomad4 NFE AF: 0.0602

Gnomad4 OTH AF: 0.0729

Alfa AF: 0.0574 Hom.: 349

Bravo AF: 0.0897

Asia WGS AF: 0.0360 AC: 126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.66
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17126243; hg19: chr11-122049675; COSMIC: COSV73190213;