Variant 11-122152392-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The ENST00000534782.4(MIR100HG):n.387+27944A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00459 in 463,940 control chromosomes in the GnomAD database, including 36 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 0.011 ( 30 hom., cov: 33)

Exomes 𝑓: 0.0014 ( 6 hom. )

Consequence

MIR100HG
ENST00000534782.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.930

Variant links:

Genes affected

MIR100HG (HGNC:):

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=-0.84).

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0112 (1708/152300) while in subpopulation AFR AF= 0.039 (1620/41552). AF 95% confidence interval is 0.0374. There are 30 homozygotes in gnomad4. There are 838 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 30 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
MIR100HG	NR_024430.2 linkuse as main transcript	n.491+3159A>G	intron_variant
MIR100HG	NR_137179.1 linkuse as main transcript	n.445+3159A>G	intron_variant
MIR100HG	NR_137180.1 linkuse as main transcript	n.503+3159A>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
MIR100HG	ENST00000534782.4 linkuse as main transcript	n.387+27944A>G	intron_variant	1
MIR100HG	ENST00000534297.2 linkuse as main transcript	n.185+3159A>G	intron_variant	4
MIR100HG	ENST00000637700.1 linkuse as main transcript	n.681+3159A>G	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.0112

AC:

1703

AN:

152182

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0390

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00380

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000235

Gnomad OTH

AF:

0.00574

GnomAD4 exome

AF:

0.00136

AC:

423

AN:

311640

Hom.:

AF XY:

0.00103

AC XY:

180

AN XY:

174614

show subpopulations

Gnomad4 AFR exome

AF:

0.0428

Gnomad4 AMR exome

AF:

0.00153

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000354

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000774

Gnomad4 OTH exome

AF:

0.00133

GnomAD4 genome

AF:

0.0112

AC:

1708

AN:

152300

Hom.:

Cov.:

AF XY:

0.0113

AC XY:

838

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.0390

Gnomad4 AMR

AF:

0.00379

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000235

Gnomad4 OTH

AF:

0.00568

Alfa

AF:

0.00970

Hom.:

Bravo

AF:

0.0129

Asia WGS

AF:

0.00144

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

5.0

DANN

Benign

0.65

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