rs6879219

Variant names:

• chr5-55220693-G-A
• rs6879219
• NM_001190787.3:c.831C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-55220693-G-A
• chr5-55220693-G-C

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_001190787.3(MCIDAS):​c.831C>T​(p.Cys277Cys) 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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:5
• Conservation: PhyloP100: 0.694
• Publications: 13 publications found

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 Gene-Disease associations (from GenCC):

• ciliary dyskinesia, primary, 42

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, ClinGen, PanelApp Australia
• primary ciliary dyskinesia

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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 rank	MANE	Protein	UniProt
MCIDAS	NM_001190787.3	c.831C>T	p.Cys277Cys	synonymous_variant	Exon 7 of 7	ENST00000513312.3	NP_001177716.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MCIDAS	ENST00000513312.3	c.831C>T	p.Cys277Cys	synonymous_variant	Exon 7 of 7	1	NM_001190787.3	ENSP00000426359.1
MCIDAS	ENST00000513468.5	n.*295C>T		non_coding_transcript_exon_variant	Exon 7 of 7	5		ENSP00000422165.1
MCIDAS	ENST00000513468.5	n.*295C>T		3_prime_UTR_variant	Exon 7 of 7	5		ENSP00000422165.1

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81089 AN: 151952 Hom.: 22648 Cov.: 33

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

GnomAD2 exomes AF: 0.583 AC: 78419 AN: 134596 AF XY: 0.592

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 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.: 76 AF XY: 0.619 AC XY: 422943 AN XY: 682828

African (AFR) AF: 0.341 AC: 10765 AN: 31594

American (AMR) AF: 0.548 AC: 19553 AN: 35700

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 17216 AN: 25178

East Asian (EAS) AF: 0.482 AC: 17207 AN: 35732

South Asian (SAS) AF: 0.617 AC: 48915 AN: 79236

European-Finnish (FIN) AF: 0.538 AC: 18215 AN: 33888

Middle Eastern (MID) AF: 0.601 AC: 3420 AN: 5690

European-Non Finnish (NFE) AF: 0.635 AC: 684588 AN: 1078846

Other (OTH) AF: 0.598 AC: 34616 AN: 57900

GnomAD4 genome AF: 0.533 AC: 81124 AN: 152070 Hom.: 22654 Cov.: 33 AF XY: 0.530 AC XY: 39382 AN XY: 74322

African (AFR) AF: 0.350 AC: 14544 AN: 41500

American (AMR) AF: 0.544 AC: 8325 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2359 AN: 3470

East Asian (EAS) AF: 0.475 AC: 2444 AN: 5142

South Asian (SAS) AF: 0.606 AC: 2927 AN: 4828

European-Finnish (FIN) AF: 0.529 AC: 5591 AN: 10564

Middle Eastern (MID) AF: 0.661 AC: 193 AN: 292

European-Non Finnish (NFE) AF: 0.634 AC: 43049 AN: 67954

Other (OTH) AF: 0.538 AC: 1137 AN: 2112

Alfa AF: 0.607 Hom.: 20404

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

Submissions by phenotype

not provided Benign:2

May 04, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

not specified Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Ciliary dyskinesia, primary, 42 Benign:1

Sep 05, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	12
DANN	Benign	0.89
PhyloP100		0.69
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6879219; hg19: chr5-54516521; COSMIC: COSV72813211; COSMIC: COSV72813211;