Variant rs11552068 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_004928.3(CFAP410):c.684T>C(p.Asp228Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00915 in 1,609,542 control chromosomes in the GnomAD database, including 711 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.038 ( 335 hom., cov: 34)

Exomes 𝑓: 0.0061 ( 376 hom. )

Consequence

CFAP410
NM_004928.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.228

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 links:

CFAP410 (HGNC:):

CFAP410 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant 21-44330285-A-G is Benign according to our data. Variant chr21-44330285-A-G is described in ClinVar as [Benign]. Clinvar id is 259588.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.228 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP410	NM_004928.3 linkuse as main transcript	c.684T>C	p.Asp228Asp	synonymous_variant	7/7	ENST00000339818.9	NP_004919.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP410	ENST00000339818.9 linkuse as main transcript	c.684T>C	p.Asp228Asp	synonymous_variant	7/7	1	NM_004928.3	ENSP00000344566.4		O43822-1

Frequencies

GnomAD3 genomes

AF:

0.0382

AC:

5809

AN:

152174

Hom.:

332

Cov.:

show subpopulations

Gnomad AFR

AF:

0.121

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0303

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0293

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.00490

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.000559

Gnomad OTH

AF:

0.0349

GnomAD3 exomes

AF:

0.0182

AC:

4276

AN:

234990

Hom.:

179

AF XY:

0.0139

AC XY:

1797

AN XY:

128906

show subpopulations

Gnomad AFR exome

AF:

0.127

Gnomad AMR exome

AF:

0.0492

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0284

Gnomad SAS exome

AF:

0.00107

Gnomad FIN exome

AF:

0.00429

Gnomad NFE exome

AF:

0.000512

Gnomad OTH exome

AF:

0.0101

GnomAD4 exome

AF:

0.00609

AC:

8880

AN:

1457250

Hom.:

376

Cov.:

AF XY:

0.00538

AC XY:

3897

AN XY:

724720

show subpopulations

Gnomad4 AFR exome

AF:

0.128

Gnomad4 AMR exome

AF:

0.0479

Gnomad4 ASJ exome

AF:

0.0000384

Gnomad4 EAS exome

AF:

0.0229

Gnomad4 SAS exome

AF:

0.00117

Gnomad4 FIN exome

AF:

0.00455

Gnomad4 NFE exome

AF:

0.000248

Gnomad4 OTH exome

AF:

0.0143

GnomAD4 genome

AF:

0.0384

AC:

5841

AN:

152292

Hom.:

335

Cov.:

AF XY:

0.0377

AC XY:

2806

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.121

Gnomad4 AMR

AF:

0.0306

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0293

Gnomad4 SAS

AF:

0.00186

Gnomad4 FIN

AF:

0.00490

Gnomad4 NFE

AF:

0.000544

Gnomad4 OTH

AF:

0.0355

Alfa

AF:

0.0108

Hom.:

Bravo

AF:

0.0445

Asia WGS

AF:

0.0280

AC:

AN:

3478

EpiCase

AF:

0.000654

EpiControl

AF:

0.000238

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 04, 2021	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

3.6

DANN

Benign

0.68

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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