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GeneBe

rs149428354

chr17-9632898-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_145054.5(CFAP52):c.1185C>T(p.Asp395=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00528 in 1,614,020 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0043 ( 4 hom., cov: 32)
Exomes 𝑓: 0.0054 ( 30 hom. )

Consequence

CFAP52
NM_145054.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.33
Variant links:
Genes affected
CFAP52 (HGNC:16053): (cilia and flagella associated protein 52) WD repeat-containing proteins, such as WDR16, play crucial roles in a wide range of physiologic functions, including signal transduction, RNA processing, remodeling the cytoskeleton, regulation of vesicular traffic, and cell division (Silva et al., 2005 [PubMed 15967112]).[supplied by OMIM, Mar 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 17-9632898-C-T is Benign according to our data. Variant chr17-9632898-C-T is described in ClinVar as [Benign]. Clinvar id is 544339.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-2.33 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 4 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CFAP52NM_145054.5 linkuse as main transcriptc.1185C>T p.Asp395= synonymous_variant 10/14 ENST00000352665.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CFAP52ENST00000352665.10 linkuse as main transcriptc.1185C>T p.Asp395= synonymous_variant 10/141 NM_145054.5 P1Q8N1V2-1
CFAP52ENST00000396219.7 linkuse as main transcriptc.981C>T p.Asp327= synonymous_variant 9/132 Q8N1V2-3
CFAP52ENST00000576630.5 linkuse as main transcriptc.*1246C>T 3_prime_UTR_variant, NMD_transcript_variant 11/152

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00431
AC:
656
AN:
152206
Hom.:
4
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00123
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00419
Gnomad ASJ
AF:
0.0199
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.000620
Gnomad FIN
AF:
0.00283
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00628
Gnomad OTH
AF:
0.00525
GnomAD3 exomes
AF:
0.00429
AC:
1078
AN:
251226
Hom.:
7
AF XY:
0.00438
AC XY:
595
AN XY:
135780
show subpopulations
Gnomad AFR exome
AF:
0.000800
Gnomad AMR exome
AF:
0.00171
Gnomad ASJ exome
AF:
0.0231
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000555
Gnomad FIN exome
AF:
0.00310
Gnomad NFE exome
AF:
0.00584
Gnomad OTH exome
AF:
0.00408
GnomAD4 exome
AF:
0.00538
AC:
7869
AN:
1461696
Hom.:
30
Cov.:
30
AF XY:
0.00535
AC XY:
3887
AN XY:
727130
show subpopulations
Gnomad4 AFR exome
AF:
0.000896
Gnomad4 AMR exome
AF:
0.00190
Gnomad4 ASJ exome
AF:
0.0241
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000615
Gnomad4 FIN exome
AF:
0.00373
Gnomad4 NFE exome
AF:
0.00585
Gnomad4 OTH exome
AF:
0.00603
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00431
AC:
656
AN:
152324
Hom.:
4
Cov.:
32
AF XY:
0.00408
AC XY:
304
AN XY:
74482
show subpopulations
Gnomad4 AFR
AF:
0.00123
Gnomad4 AMR
AF:
0.00418
Gnomad4 ASJ
AF:
0.0199
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.000621
Gnomad4 FIN
AF:
0.00283
Gnomad4 NFE
AF:
0.00628
Gnomad4 OTH
AF:
0.00520
Alfa
AF:
0.00656
Hom.:
1
Bravo
AF:
0.00450
EpiCase
AF:
0.00540
EpiControl
AF:
0.00439

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Situs inversus Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeNov 10, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
0.31
Dann
Benign
0.40

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.16
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.

Other links and lift over

dbSNP: rs149428354; hg19: chr17-9536215; API