rs11604461

Variant names:

• chr11-122163292-T-C
• rs11604461
• ENST00000534782.4:n.387+17044A>G

Variant summary

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

The ENST00000534782.4(MIR100HG):​n.387+17044A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0985 in 152,062 control chromosomes in the GnomAD database, including 971 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 0.099 (971 hom., cov: 32)
• Consequence: MIR100HG ENST00000534782.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156
• Publications: 6 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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR100HG	NR_024430.2	n.410-7660A>G		intron_variant	Intron 2 of 3
MIR100HG	NR_137179.1	n.364-7660A>G		intron_variant	Intron 3 of 4
MIR100HG	NR_137180.1	n.422-7660A>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000534782.4	n.387+17044A>G		intron_variant	Intron 2 of 2	1
MIR100HG	ENST00000532350.6	n.388-7660A>G		intron_variant	Intron 2 of 2	5
MIR100HG	ENST00000533109.6	n.917-7660A>G		intron_variant	Intron 6 of 6	5

Frequencies

GnomAD3 genomes AF: 0.0987 AC: 14995 AN: 151944 Hom.: 974 Cov.: 32

Gnomad AFR AF: 0.0245

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0964

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.0985 AC: 14980 AN: 152062 Hom.: 971 Cov.: 32 AF XY: 0.0977 AC XY: 7263 AN XY: 74316

African (AFR) AF: 0.0244 AC: 1014 AN: 41530

American (AMR) AF: 0.107 AC: 1634 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 483 AN: 3470

East Asian (EAS) AF: 0.213 AC: 1096 AN: 5144

South Asian (SAS) AF: 0.142 AC: 683 AN: 4804

European-Finnish (FIN) AF: 0.0964 AC: 1020 AN: 10586

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8676 AN: 67948

Other (OTH) AF: 0.132 AC: 279 AN: 2114

Alfa AF: 0.119 Hom.: 1559

Bravo AF: 0.0969

Asia WGS AF: 0.163 AC: 565 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.2
DANN	Benign	0.74
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs11604461; hg19: chr11-122034000;