rs531897

Variant names:

• chr11-122142461-C-T
• rs531897
• ENST00000534782.4:n.387+37875G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000534782.4(MIR100HG):​n.387+37875G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.445
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000534782.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR100HG	NR_024430.2		n.491+13090G>A		intron	N/A
	MIR100HG	NR_137179.1		n.445+13090G>A		intron	N/A
	MIR100HG	NR_137180.1		n.503+13090G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR100HG	ENST00000534782.4	TSL:1	n.387+37875G>A		intron	N/A
	MIR100HG	ENST00000534297.2	TSL:4	n.185+13090G>A		intron	N/A
	MIR100HG	ENST00000637700.1	TSL:5	n.681+13090G>A		intron	N/A

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

African (AFR) AF: 0.634 AC: 26285 AN: 41484

American (AMR) AF: 0.717 AC: 10970 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2267 AN: 3472

East Asian (EAS) AF: 0.653 AC: 3377 AN: 5168

South Asian (SAS) AF: 0.495 AC: 2382 AN: 4814

European-Finnish (FIN) AF: 0.760 AC: 8051 AN: 10598

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46133 AN: 67996

Other (OTH) AF: 0.673 AC: 1421 AN: 2112

Alfa AF: 0.674 Hom.: 94077

Bravo AF: 0.669

Asia WGS AF: 0.590 AC: 2051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.69
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs531897; hg19: chr11-122013169;