11-122043217-G-T

Variant names:

• chr11-122043217-G-T
• rs7949079
• ENST00000530955.2:n.257-14372C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000531470.3(MIR100HG):​n.853-9755C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,040 control chromosomes in the GnomAD database, including 3,342 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 0.20 (3342 hom., cov: 33)
• Consequence: MIR100HG ENST00000531470.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR100HG	NR_137178.1	n.865-9755C>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR100HG	ENST00000530955.2	n.257-14372C>A		intron_variant	Intron 1 of 1	5
MIR100HG	ENST00000531470.3	n.853-9755C>A		intron_variant	Intron 5 of 7	4
MIR100HG	ENST00000532319.2	n.2375-9755C>A		intron_variant	Intron 2 of 3	4

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30664 AN: 151922 Hom.: 3338 Cov.: 33

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.0886

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.202 AC: 30698 AN: 152040 Hom.: 3342 Cov.: 33 AF XY: 0.201 AC XY: 14928 AN XY: 74300

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.0890

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.228

Alfa AF: 0.228 Hom.: 8558

Bravo AF: 0.192

Asia WGS AF: 0.142 AC: 495 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.57
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7949079; hg19: chr11-121913925;