ENST00000527474.5:n.899-22938A>C

Variant names:

• chr11-122203336-T-G
• rs10892819
• ENST00000527474.5:n.899-22938A>C

Variant summary

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

The ENST00000527474.5(MIR100HG):​n.899-22938A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,084 control chromosomes in the GnomAD database, including 6,326 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 0.28 (6326 hom., cov: 32)
• Consequence: MIR100HG ENST00000527474.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 4 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=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR100HG	NR_137179.1	n.301-22938A>C		intron_variant	Intron 2 of 4
MIR100HG	NR_137180.1	n.359-22938A>C		intron_variant	Intron 2 of 4
MIR100HG	NR_137192.1	n.614-22938A>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000527474.5	n.899-22938A>C		intron_variant	Intron 3 of 3	1
MIR100HG	ENST00000647967.2	n.408A>C		non_coding_transcript_exon_variant	Exon 2 of 3
MIR100HG	ENST00000654571.2	n.567A>C		non_coding_transcript_exon_variant	Exon 3 of 5

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42239 AN: 151966 Hom.: 6325 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.278 AC: 42246 AN: 152084 Hom.: 6326 Cov.: 32 AF XY: 0.281 AC XY: 20871 AN XY: 74334

African (AFR) AF: 0.164 AC: 6822 AN: 41530

American (AMR) AF: 0.283 AC: 4323 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1170 AN: 3466

East Asian (EAS) AF: 0.265 AC: 1368 AN: 5156

South Asian (SAS) AF: 0.284 AC: 1368 AN: 4810

European-Finnish (FIN) AF: 0.384 AC: 4050 AN: 10554

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22134 AN: 67968

Other (OTH) AF: 0.295 AC: 623 AN: 2112

Alfa AF: 0.297 Hom.: 4112

Bravo AF: 0.266

Asia WGS AF: 0.281 AC: 974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	1.7
DANN	Benign	0.81
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs10892819; hg19: chr11-122074044;