rs547008

Variant names:

• chr11-122147153-G-A
• rs547008
• ENST00000534782.4:n.387+33183C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-122147153-G-A
• chr11-122147153-G-C
• chr11-122147153-G-T

Variant summary

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

The ENST00000534782.4(MIR100HG):​n.387+33183C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,074 control chromosomes in the GnomAD database, including 1,298 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 0.13 (1298 hom., cov: 32)
• Consequence: MIR100HG ENST00000534782.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482
• Publications: 7 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.241 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR100HG	NR_024430.2		n.491+8398C>T		intron	N/A
	MIR100HG	NR_137179.1		n.445+8398C>T		intron	N/A
	MIR100HG	NR_137180.1		n.503+8398C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR100HG	ENST00000534782.4	TSL:1	n.387+33183C>T		intron	N/A
	MIR100HG	ENST00000534297.2	TSL:4	n.185+8398C>T		intron	N/A
	MIR100HG	ENST00000637700.1	TSL:5	n.681+8398C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19102 AN: 151956 Hom.: 1302 Cov.: 32

Gnomad AFR AF: 0.0903

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.125 AC: 19085 AN: 152074 Hom.: 1298 Cov.: 32 AF XY: 0.127 AC XY: 9465 AN XY: 74344

African (AFR) AF: 0.0900 AC: 3736 AN: 41498

American (AMR) AF: 0.111 AC: 1692 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3470

East Asian (EAS) AF: 0.253 AC: 1306 AN: 5168

South Asian (SAS) AF: 0.248 AC: 1191 AN: 4812

European-Finnish (FIN) AF: 0.117 AC: 1237 AN: 10562

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9063 AN: 67970

Other (OTH) AF: 0.118 AC: 247 AN: 2100

Alfa AF: 0.131 Hom.: 2542

Bravo AF: 0.122

Asia WGS AF: 0.255 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.64
DANN	Benign	0.60
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs547008; hg19: chr11-122017861;