Variant 10-72368095-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001195518.2(MICU1):c.*100C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 1,261,036 control chromosomes in the GnomAD database, including 236,303 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.54 ( 22841 hom., cov: 30)

Exomes 𝑓: 0.61 ( 213462 hom. )

Consequence

MICU1
NM_001195518.2 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.641

Variant links:

Genes affected

MICU1 (HGNC:1530): (mitochondrial calcium uptake 1) This gene encodes an essential regulator of mitochondrial Ca2+ uptake under basal conditions. The encoded protein interacts with the mitochondrial calcium uniporter, a mitochondrial inner membrane Ca2+ channel, and is essential in preventing mitochondrial Ca2+ overload, which can cause excessive production of reactive oxygen species and cell stress. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Mar 2013]

MICU1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 10-72368095-G-A is Benign according to our data. Variant chr10-72368095-G-A is described in ClinVar as [Benign]. Clinvar id is 1291021.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MICU1	NM_001195518.2 linkuse as main transcript	c.*100C>T		3_prime_UTR_variant	12/12	ENST00000361114.10	NP_001182447.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MICU1	ENST00000361114.10 linkuse as main transcript	c.*100C>T		3_prime_UTR_variant	12/12	1	NM_001195518.2	ENSP00000354415	P4	Q9BPX6-1

Frequencies

GnomAD3 genomes

AF:

0.538

AC:

81596

AN:

151772

Hom.:

22825

Cov.:

show subpopulations

Gnomad AFR

AF:

0.465

Gnomad AMI

AF:

0.649

Gnomad AMR

AF:

0.497

Gnomad ASJ

AF:

0.507

Gnomad EAS

AF:

0.159

Gnomad SAS

AF:

0.498

Gnomad FIN

AF:

0.467

Gnomad MID

AF:

0.639

Gnomad NFE

AF:

0.632

Gnomad OTH

AF:

0.565

GnomAD4 exome

AF:

0.612

AC:

678795

AN:

1109146

Hom.:

213462

Cov.:

AF XY:

0.610

AC XY:

333581

AN XY:

546844

show subpopulations

Gnomad4 AFR exome

AF:

0.455

Gnomad4 AMR exome

AF:

0.454

Gnomad4 ASJ exome

AF:

0.524

Gnomad4 EAS exome

AF:

0.191

Gnomad4 SAS exome

AF:

0.529

Gnomad4 FIN exome

AF:

0.496

Gnomad4 NFE exome

AF:

0.655

Gnomad4 OTH exome

AF:

0.585

GnomAD4 genome

AF:

0.538

AC:

81646

AN:

151890

Hom.:

22841

Cov.:

AF XY:

0.526

AC XY:

39006

AN XY:

74226

show subpopulations

Gnomad4 AFR

AF:

0.466

Gnomad4 AMR

AF:

0.497

Gnomad4 ASJ

AF:

0.507

Gnomad4 EAS

AF:

0.158

Gnomad4 SAS

AF:

0.499

Gnomad4 FIN

AF:

0.467

Gnomad4 NFE

AF:

0.632

Gnomad4 OTH

AF:

0.559

Alfa

AF:

0.609

Hom.:

47430

Bravo

AF:

0.535

Asia WGS

AF:

0.320

AC:

1115

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 23, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.86

DANN

Benign

0.49

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over