Variant rs547008 details in Genebe, Genetics Data Aggregator

Variant summary

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

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.482

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]

MIR100HG links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
MIR100HG	NR_024430.2 link	n.491+8398C>T	intron_variant
MIR100HG	NR_137179.1 link	n.445+8398C>T	intron_variant
MIR100HG	NR_137180.1 link	n.503+8398C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
MIR100HG	ENST00000534782.4 link	n.387+33183C>T	intron_variant	1
MIR100HG	ENST00000534297.2 link	n.185+8398C>T	intron_variant	4
MIR100HG	ENST00000637700.1 link	n.681+8398C>T	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.126

AC:

19102

AN:

151956

Hom.:

1302

Cov.:

show subpopulations

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.:

AF XY:

0.127

AC XY:

9465

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.0900

Gnomad4 AMR

AF:

0.111

Gnomad4 ASJ

AF:

0.136

Gnomad4 EAS

AF:

0.253

Gnomad4 SAS

AF:

0.248

Gnomad4 FIN

AF:

0.117

Gnomad4 NFE

AF:

0.133

Gnomad4 OTH

AF:

0.118

Alfa

AF:

0.136

Hom.:

713

Bravo

AF:

0.122

Asia WGS

AF:

0.255

AC:

890

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

0.64

DANN

Benign

0.60

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over