Variant 5-55220693-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001190787.3(MCIDAS):c.831C>T(p.Cys277=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 1,535,834 control chromosomes in the GnomAD database, including 289,311 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.53 ( 22654 hom., cov: 33)

Exomes 𝑓: 0.62 ( 266657 hom. )

Consequence

MCIDAS
NM_001190787.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 0.694

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 5-55220693-G-A is Benign according to our data. Variant chr5-55220693-G-A is described in ClinVar as [Benign]. Clinvar id is 403074.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.694 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.628 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.831C>T	p.Cys277=	synonymous_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.831C>T	p.Cys277=	synonymous_variant	7/7	1	NM_001190787.3	P1
MCIDAS	ENST00000513468.5 linkuse as main transcript	c.*295C>T		3_prime_UTR_variant, NMD_transcript_variant	7/7	5

Frequencies

GnomAD3 genomes

AF:

0.534

AC:

81089

AN:

151952

Hom.:

22648

Cov.:

show subpopulations

Gnomad AFR

AF:

0.351

Gnomad AMI

AF:

0.610

Gnomad AMR

AF:

0.544

Gnomad ASJ

AF:

0.680

Gnomad EAS

AF:

0.476

Gnomad SAS

AF:

0.605

Gnomad FIN

AF:

0.529

Gnomad MID

AF:

0.659

Gnomad NFE

AF:

0.634

Gnomad OTH

AF:

0.536

GnomAD3 exomes

AF:

0.583

AC:

78419

AN:

134596

Hom.:

23396

AF XY:

0.592

AC XY:

43390

AN XY:

73306

show subpopulations

Gnomad AFR exome

AF:

0.348

Gnomad AMR exome

AF:

0.540

Gnomad ASJ exome

AF:

0.677

Gnomad EAS exome

AF:

0.462

Gnomad SAS exome

AF:

0.613

Gnomad FIN exome

AF:

0.543

Gnomad NFE exome

AF:

0.631

Gnomad OTH exome

AF:

0.589

GnomAD4 exome

AF:

0.618

AC:

854495

AN:

1383764

Hom.:

266657

Cov.:

AF XY:

0.619

AC XY:

422943

AN XY:

682828

show subpopulations

Gnomad4 AFR exome

AF:

0.341

Gnomad4 AMR exome

AF:

0.548

Gnomad4 ASJ exome

AF:

0.684

Gnomad4 EAS exome

AF:

0.482

Gnomad4 SAS exome

AF:

0.617

Gnomad4 FIN exome

AF:

0.538

Gnomad4 NFE exome

AF:

0.635

Gnomad4 OTH exome

AF:

0.598

GnomAD4 genome

AF:

0.533

AC:

81124

AN:

152070

Hom.:

22654

Cov.:

AF XY:

0.530

AC XY:

39382

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.350

Gnomad4 AMR

AF:

0.544

Gnomad4 ASJ

AF:

0.680

Gnomad4 EAS

AF:

0.475

Gnomad4 SAS

AF:

0.606

Gnomad4 FIN

AF:

0.529

Gnomad4 NFE

AF:

0.634

Gnomad4 OTH

AF:

0.538

Alfa

AF:

0.603

Hom.:

10889

Bravo

AF:

0.523

Asia WGS

AF:

0.512

AC:

1779

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Primary ciliary dyskinesia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Ciliary dyskinesia, primary, 42

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

DANN

Benign

0.89

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