Variant 5-55220358-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001190787.3(MCIDAS):c.*8T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00905 in 1,529,672 control chromosomes in the GnomAD database, including 117 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0086 ( 18 hom., cov: 33)

Exomes 𝑓: 0.0091 ( 99 hom. )

Consequence

MCIDAS
NM_001190787.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.538

Variant links:

Genes affected

MCIDAS (HGNC:40050): (multiciliate differentiation and DNA synthesis associated cell cycle protein) This gene encodes a member of the geminin family of proteins. The encoded nuclear protein is required for the generation of multiciliated cells in respiratory epithelium. Mutations in this gene cause a rare mucociliary clearance disorder associated with recurring respiratory infections in human patients, known as reduced generation of multiple motile cilia (RGMC). [provided by RefSeq, Sep 2016]

MCIDAS links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 5-55220358-A-G is Benign according to our data. Variant chr5-55220358-A-G is described in ClinVar as [Benign]. Clinvar id is 1287962.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MCIDAS	NM_001190787.3 linkuse as main transcript	c.*8T>C		3_prime_UTR_variant	7/7	ENST00000513312.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MCIDAS	ENST00000513312.3 linkuse as main transcript	c.*8T>C		3_prime_UTR_variant	7/7	1	NM_001190787.3	P1
MCIDAS	ENST00000513468.5 linkuse as main transcript	c.*630T>C		3_prime_UTR_variant, NMD_transcript_variant	7/7	5

Frequencies

GnomAD3 genomes

AF:

0.00862

AC:

1312

AN:

152200

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00162

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00563

Gnomad ASJ

AF:

0.0187

Gnomad EAS

AF:

0.0653

Gnomad SAS

AF:

0.00601

Gnomad FIN

AF:

0.00791

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00911

Gnomad OTH

AF:

0.0100

GnomAD3 exomes

AF:

0.0115

AC:

1519

AN:

132050

Hom.:

AF XY:

0.0115

AC XY:

823

AN XY:

71736

show subpopulations

Gnomad AFR exome

AF:

0.00140

Gnomad AMR exome

AF:

0.00300

Gnomad ASJ exome

AF:

0.0176

Gnomad EAS exome

AF:

0.0641

Gnomad SAS exome

AF:

0.00431

Gnomad FIN exome

AF:

0.0106

Gnomad NFE exome

AF:

0.00857

Gnomad OTH exome

AF:

0.00786

GnomAD4 exome

AF:

0.00910

AC:

12535

AN:

1377354

Hom.:

Cov.:

AF XY:

0.00906

AC XY:

6145

AN XY:

678504

show subpopulations

Gnomad4 AFR exome

AF:

0.00105

Gnomad4 AMR exome

AF:

0.00295

Gnomad4 ASJ exome

AF:

0.0169

Gnomad4 EAS exome

AF:

0.0526

Gnomad4 SAS exome

AF:

0.00401

Gnomad4 FIN exome

AF:

0.00999

Gnomad4 NFE exome

AF:

0.00819

Gnomad4 OTH exome

AF:

0.0111

GnomAD4 genome

AF:

0.00861

AC:

1311

AN:

152318

Hom.:

Cov.:

AF XY:

0.00865

AC XY:

644

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.00161

Gnomad4 AMR

AF:

0.00562

Gnomad4 ASJ

AF:

0.0187

Gnomad4 EAS

AF:

0.0653

Gnomad4 SAS

AF:

0.00601

Gnomad4 FIN

AF:

0.00791

Gnomad4 NFE

AF:

0.00911

Gnomad4 OTH

AF:

0.00992

Alfa

AF:

0.00938

Hom.:

Bravo

AF:

0.00834

Asia WGS

AF:

0.0330

AC:

116

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.5

DANN

Benign

0.76

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