ENST00000530955.3:n.682+17498C>T

Variant names:

• chr11-122083949-G-A
• rs7121446
• ENST00000530955.3:n.682+17498C>T

Variant summary

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

The ENST00000530955.3(MIR100HG):​n.682+17498C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 151,968 control chromosomes in the GnomAD database, including 5,786 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 0.26 (5786 hom., cov: 31)
• Consequence: MIR100HG ENST00000530955.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234
• Publications: 12 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 (AFR) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR100HG	NR_137178.1	n.473+16425C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000530955.3	n.682+17498C>T		intron_variant	Intron 1 of 1	5
MIR100HG	ENST00000532319.2	n.119+16425C>T		intron_variant	Intron 1 of 3	4
MIR100HG	ENST00000636654.1	n.75+16425C>T		intron_variant	Intron 1 of 7	5

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39698 AN: 151850 Hom.: 5768 Cov.: 31

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.0516

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.262 AC: 39766 AN: 151968 Hom.: 5786 Cov.: 31 AF XY: 0.257 AC XY: 19094 AN XY: 74272

African (AFR) AF: 0.390 AC: 16167 AN: 41420

American (AMR) AF: 0.181 AC: 2765 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 699 AN: 3462

East Asian (EAS) AF: 0.0514 AC: 266 AN: 5178

South Asian (SAS) AF: 0.217 AC: 1045 AN: 4812

European-Finnish (FIN) AF: 0.208 AC: 2198 AN: 10560

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.232 AC: 15769 AN: 67950

Other (OTH) AF: 0.273 AC: 575 AN: 2108

Alfa AF: 0.236 Hom.: 19046

Bravo AF: 0.267

Asia WGS AF: 0.172 AC: 598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.29
DANN	Benign	0.23
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs7121446; hg19: chr11-121954657;