rs1834306

Positions:

• chr11-122152479-A-G

Variant summary

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

The ENST00000534782.4(MIR100HG):​n.387+27857T>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 0.494 in 152,110 control chromosomes in the GnomAD database, including 19,646 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 0.49 (19646 hom., cov: 33)
• Consequence: MIR100HG ENST00000534782.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370

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 (NFE) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR100HG	NR_024430.2	n.491+3072T>C		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137179.1	n.445+3072T>C		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137180.1	n.503+3072T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR100HG	ENST00000534782.4	n.387+27857T>C		intron_variant, non_coding_transcript_variant		1
MIR100HG	ENST00000534297.2	n.185+3072T>C		intron_variant, non_coding_transcript_variant		4
MIR100HG	ENST00000637700.1	n.681+3072T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75084 AN: 151992 Hom.: 19636 Cov.: 33

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.494 AC: 75122 AN: 152110 Hom.: 19646 Cov.: 33 AF XY: 0.496 AC XY: 36880 AN XY: 74340

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.704

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.503

Alfa AF: 0.542 Hom.: 4655

Bravo AF: 0.464

Asia WGS AF: 0.462 AC: 1605 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	0.61
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1834306; hg19: chr11-122023187; COSMIC: COSV66115428;