rs588354

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000534782.4(MIR100HG):​n.387+7298C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0552 in 152,156 control chromosomes in the GnomAD database, including 770 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 0.055 ( 770 hom., cov: 33)

Consequence

MIR100HG
ENST00000534782.4 intron

Scores

1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0690
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MIR100HGNR_024430.2 linkn.409+7298C>T intron_variant Intron 2 of 3
MIR100HGNR_137179.1 linkn.363+7298C>T intron_variant Intron 3 of 4
MIR100HGNR_137180.1 linkn.421+7298C>T intron_variant Intron 3 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MIR100HGENST00000534782.4 linkn.387+7298C>T intron_variant Intron 2 of 2 1
MIR100HGENST00000532350.6 linkn.387+7298C>T intron_variant Intron 2 of 2 5
MIR100HGENST00000533109.6 linkn.916+7298C>T intron_variant Intron 6 of 6 5

Frequencies

GnomAD3 genomes
AF:
0.0551
AC:
8378
AN:
152038
Hom.:
765
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.191
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0215
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000623
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.000853
Gnomad OTH
AF:
0.0430
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0552
AC:
8402
AN:
152156
Hom.:
770
Cov.:
33
AF XY:
0.0531
AC XY:
3948
AN XY:
74386
show subpopulations
Gnomad4 AFR
AF:
0.191
Gnomad4 AMR
AF:
0.0215
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000623
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000853
Gnomad4 OTH
AF:
0.0426
Alfa
AF:
0.0356
Hom.:
63
Bravo
AF:
0.0630

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
3.5

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs588354; hg19: chr11-122043746; API