rs531897

chr11-122142461-C-T

Variant summary

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

The ENST00000534782.4(MIR100HG):n.387+37875G>A 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 0.669 in 152,148 control chromosomes in the GnomAD database, including 34,203 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 0.67 (34203 hom., cov: 33)
• Consequence: MIR100HG ENST00000534782.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.445

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR100HG	NR_024430.2	n.491+13090G>A		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137179.1	n.445+13090G>A		intron_variant, non_coding_transcript_variant
MIR100HG	NR_137180.1	n.503+13090G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR100HG	ENST00000534782.4	n.387+37875G>A		intron_variant, non_coding_transcript_variant		1
MIR100HG	ENST00000534297.2	n.185+13090G>A		intron_variant, non_coding_transcript_variant		4
MIR100HG	ENST00000637700.1	n.681+13090G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101665 AN: 152030 Hom.: 34169 Cov.: 33

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.669 AC: 101751 AN: 152148 Hom.: 34203 Cov.: 33 AF XY: 0.670 AC XY: 49854 AN XY: 74386

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.653

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.673

Alfa AF: 0.677 Hom.: 58673

Bravo AF: 0.669

Asia WGS AF: 0.590 AC: 2051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.3
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs531897; hg19: chr11-122013169;