chr21-44339162-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_004928.3(CFAP410):c.33G>A(p.Arg11Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 1,470,992 control chromosomes in the GnomAD database, including 42,087 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. R11R) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.28 ( 6648 hom., cov: 31)

Exomes 𝑓: 0.22 ( 35439 hom. )

Consequence

CFAP410
NM_004928.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.0680

Publications

19 publications found

Variant links:

Genes affected

CFAP410 (HGNC:1260): (cilia and flagella associated protein 410) Four alternatively spliced transcript variants encoding four different isoforms have been found for this nuclear gene. All isoforms contain leucine-rich repeats. Three of these isoforms are mitochondrial proteins and one of them lacks the target peptide, so is not located in mitochondrion. This gene is down-regulated in Down syndrome (DS) brain, which may represent mitochondrial dysfunction in DS patients. [provided by RefSeq, Sep 2012]

CFAP410 Gene-Disease associations (from GenCC):

axial spondylometaphyseal dysplasia
Inheritance: AR Classification: DEFINITIVE Submitted by: G2P
amyotrophic lateral sclerosis
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
cone-rod dystrophy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

CFAP410 links:

ENSG00000232969 (HGNC:):

ENSG00000232969 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.3).

BP6

Variant 21-44339162-C-T is Benign according to our data. Variant chr21-44339162-C-T is described in ClinVar as Benign. ClinVar VariationId is 259586.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.068 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP410	NM_004928.3 link	c.33G>A	p.Arg11Arg	synonymous_variant	Exon 1 of 7	ENST00000339818.9	NP_004919.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
CFAP410	ENST00000339818.9 link	c.33G>A	p.Arg11Arg	synonymous_variant	Exon 1 of 7	1	NM_004928.3	ENSP00000344566.4	O43822-1
CFAP410	ENST00000397956.7 link	c.33G>A	p.Arg11Arg	synonymous_variant	Exon 1 of 7	1		ENSP00000381047.3	O43822-4
CFAP410	ENST00000325223.7 link	c.33G>A	p.Arg11Arg	synonymous_variant	Exon 1 of 7	1		ENSP00000317302.7	O43822-3
ENSG00000232969	ENST00000426029.1 link	n.-214C>T		upstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.278

AC:

42128

AN:

151348

Hom.:

6642

Cov.:

show subpopulations

Gnomad AFR

AF:

0.425

Gnomad AMI

AF:

0.173

Gnomad AMR

AF:

0.257

Gnomad ASJ

AF:

0.186

Gnomad EAS

AF:

0.148

Gnomad SAS

AF:

0.378

Gnomad FIN

AF:

0.184

Gnomad MID

AF:

0.293

Gnomad NFE

AF:

0.217

Gnomad OTH

AF:

0.278

GnomAD2 exomes

AF:

0.240

AC:

21903

AN:

91162

AF XY:

0.247

show subpopulations

Gnomad AFR exome

AF:

0.409

Gnomad AMR exome

AF:

0.250

Gnomad ASJ exome

AF:

0.182

Gnomad EAS exome

AF:

0.130

Gnomad FIN exome

AF:

0.192

Gnomad NFE exome

AF:

0.210

Gnomad OTH exome

AF:

0.232

GnomAD4 exome

AF:

0.225

AC:

296327

AN:

1319536

Hom.:

35439

Cov.:

AF XY:

0.228

AC XY:

148263

AN XY:

650630

show subpopulations

African (AFR)

AF:

0.432

AC:

11484

AN:

26556

American (AMR)

AF:

0.262

AC:

6546

AN:

24956

Ashkenazi Jewish (ASJ)

AF:

0.182

AC:

4209

AN:

23094

East Asian (EAS)

AF:

0.158

AC:

4432

AN:

28004

South Asian (SAS)

AF:

0.356

AC:

25219

AN:

70832

European-Finnish (FIN)

AF:

0.197

AC:

9200

AN:

46674

Middle Eastern (MID)

AF:

0.266

AC:

1412

AN:

5318

European-Non Finnish (NFE)

AF:

0.213

AC:

221259

AN:

1040058

Other (OTH)

AF:

0.233

AC:

12566

AN:

54044

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.466

Heterozygous variant carriers

9965

19930

29895

39860

49825

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8068

16136

24204

32272

40340

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.278

AC:

42175

AN:

151456

Hom.:

6648

Cov.:

AF XY:

0.277

AC XY:

20494

AN XY:

74026

show subpopulations

African (AFR)

AF:

0.425

AC:

17548

AN:

41286

American (AMR)

AF:

0.257

AC:

3928

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.186

AC:

643

AN:

3466

East Asian (EAS)

AF:

0.149

AC:

756

AN:

5076

South Asian (SAS)

AF:

0.377

AC:

1808

AN:

4790

European-Finnish (FIN)

AF:

0.184

AC:

1931

AN:

10506

Middle Eastern (MID)

AF:

0.288

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.217

AC:

14734

AN:

67754

Other (OTH)

AF:

0.278

AC:

586

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1448

2896

4343

5791

7239

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

424

848

1272

1696

2120

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.135

Hom.:

224

Bravo

AF:

0.288

Asia WGS

AF:

0.295

AC:

1012

AN:

3438

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

May 04, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

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

PreventionGenetics, part of Exact Sciences

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

-0.30

CADD

Benign

(source)

DANN

Benign

0.96

PhyloP100

0.068

PromoterAI

-0.0057

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over