chr11-122147842-T-C

Position:

• chr11-122147842-T-C

Variant summary

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

The ENST00000534782.4(MIR100HG):​n.387+32494A>G 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 0.676 in 151,864 control chromosomes in the GnomAD database, including 34,844 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 0.68 (34844 hom., cov: 29)
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR100HG	NR_024430.2	n.491+7709A>G		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137179.1	n.445+7709A>G		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137180.1	n.503+7709A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000534782.4	n.387+32494A>G		intron_variant, non_coding_transcript_variant		1
MIR100HG	ENST00000534297.2	n.185+7709A>G		intron_variant, non_coding_transcript_variant		4
MIR100HG	ENST00000637700.1	n.681+7709A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102600 AN: 151744 Hom.: 34806 Cov.: 29

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.657

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.676 AC: 102691 AN: 151864 Hom.: 34844 Cov.: 29 AF XY: 0.678 AC XY: 50307 AN XY: 74224

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.680

Alfa AF: 0.681 Hom.: 4394

Bravo AF: 0.676

Asia WGS AF: 0.615 AC: 2136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.14
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs562052; hg19: chr11-122018550;