rs150404479

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_001378189.1(CFAP57):ā€‹c.2588T>Cā€‹(p.Ile863Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0134 in 1,549,630 control chromosomes in the GnomAD database, including 184 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: š‘“ 0.0098 ( 13 hom., cov: 32)
Exomes š‘“: 0.014 ( 171 hom. )

Consequence

CFAP57
NM_001378189.1 missense

Scores

8
9

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.09
Variant links:
Genes affected
CFAP57 (HGNC:26485): (cilia and flagella associated protein 57) This protein encoded by this gene belongs to the WD repeat-containing family of proteins, which function in the formation of protein-protein complexes in a variety of biological pathways. This family member is thought to function in craniofacial development, possibly in the fusion of lip and palate. A missense mutation in this gene is associated with Van der Woude syndrome 2. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2011]
EBNA1BP2 (HGNC:15531): (EBNA1 binding protein 2) Enables RNA binding activity. Predicted to be involved in rRNA processing and ribosomal large subunit biogenesis. Located in chromosome and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.005825013).
BS1
Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.0138 (19304/1397560) while in subpopulation NFE AF= 0.0159 (17183/1078508). AF 95% confidence interval is 0.0157. There are 171 homozygotes in gnomad4_exome. There are 9221 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1486 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CFAP57NM_001378189.1 linkuse as main transcriptc.2588T>C p.Ile863Thr missense_variant 16/23 ENST00000372492.9 NP_001365118.1
LOC105378685XR_007066041.1 linkuse as main transcriptn.377-7486A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CFAP57ENST00000372492.9 linkuse as main transcriptc.2588T>C p.Ile863Thr missense_variant 16/235 NM_001378189.1 ENSP00000361570 P1Q96MR6-1

Frequencies

GnomAD3 genomes
AF:
0.00979
AC:
1488
AN:
151952
Hom.:
13
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00309
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00996
Gnomad ASJ
AF:
0.0179
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00417
Gnomad FIN
AF:
0.00359
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.0155
Gnomad OTH
AF:
0.0134
GnomAD3 exomes
AF:
0.00909
AC:
1352
AN:
148734
Hom.:
13
AF XY:
0.00931
AC XY:
746
AN XY:
80100
show subpopulations
Gnomad AFR exome
AF:
0.00178
Gnomad AMR exome
AF:
0.00573
Gnomad ASJ exome
AF:
0.0193
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00298
Gnomad FIN exome
AF:
0.00416
Gnomad NFE exome
AF:
0.0153
Gnomad OTH exome
AF:
0.0147
GnomAD4 exome
AF:
0.0138
AC:
19304
AN:
1397560
Hom.:
171
Cov.:
31
AF XY:
0.0134
AC XY:
9221
AN XY:
689310
show subpopulations
Gnomad4 AFR exome
AF:
0.00219
Gnomad4 AMR exome
AF:
0.00623
Gnomad4 ASJ exome
AF:
0.0190
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00371
Gnomad4 FIN exome
AF:
0.00516
Gnomad4 NFE exome
AF:
0.0159
Gnomad4 OTH exome
AF:
0.0129
GnomAD4 genome
AF:
0.00977
AC:
1486
AN:
152070
Hom.:
13
Cov.:
32
AF XY:
0.00881
AC XY:
655
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.00308
Gnomad4 AMR
AF:
0.00988
Gnomad4 ASJ
AF:
0.0179
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00396
Gnomad4 FIN
AF:
0.00359
Gnomad4 NFE
AF:
0.0155
Gnomad4 OTH
AF:
0.0133
Alfa
AF:
0.0129
Hom.:
10
Bravo
AF:
0.0104
TwinsUK
AF:
0.0181
AC:
67
ALSPAC
AF:
0.0140
AC:
54
ExAC
AF:
0.00560
AC:
127
Asia WGS
AF:
0.000289
AC:
1
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.41
BayesDel_addAF
Benign
-0.43
T
BayesDel_noAF
Benign
-0.37
CADD
Benign
22
DANN
Uncertain
1.0
DEOGEN2
Benign
0.087
T;T
Eigen
Benign
0.17
Eigen_PC
Uncertain
0.23
FATHMM_MKL
Uncertain
0.85
D
LIST_S2
Uncertain
0.87
D;D
MetaRNN
Benign
0.0058
T;T
MetaSVM
Benign
-1.1
T
MutationTaster
Benign
0.82
N
PrimateAI
Uncertain
0.72
T
PROVEAN
Uncertain
-3.1
D;.
REVEL
Benign
0.098
Sift
Uncertain
0.010
D;.
Sift4G
Benign
0.35
T;T
Vest4
0.34
MVP
0.14
ClinPred
0.020
T
GERP RS
4.4
Varity_R
0.21
gMVP
0.18

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs150404479; hg19: chr1-43688550; API