4-55955640-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000257287.5(CEP135):​c.472+1257C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,096 control chromosomes in the GnomAD database, including 1,536 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: 𝑓 0.13 ( 1536 hom., cov: 32)

Consequence

CEP135
ENST00000257287.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.252
Variant links:
Genes affected
CEP135 (HGNC:29086): (centrosomal protein 135) This gene encodes a centrosomal protein, which acts as a scaffolding protein during early centriole biogenesis, and is also required for centriole-centriole cohesion during interphase. Mutations in this gene are associated with autosomal recessive primary microcephaly-8. [provided by RefSeq, Jun 2012]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CEP135NM_025009.5 linkuse as main transcriptc.472+1257C>T intron_variant ENST00000257287.5 NP_079285.2
LOC124900705XR_007058124.1 linkuse as main transcriptn.198-3169G>A intron_variant, non_coding_transcript_variant
CEP135XM_006714055.4 linkuse as main transcriptc.472+1257C>T intron_variant XP_006714118.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CEP135ENST00000257287.5 linkuse as main transcriptc.472+1257C>T intron_variant 1 NM_025009.5 ENSP00000257287 P1Q66GS9-1
CEP135ENST00000422247.6 linkuse as main transcriptc.472+1257C>T intron_variant 2 ENSP00000412799 Q66GS9-2
CEP135ENST00000515081.1 linkuse as main transcriptn.106+1257C>T intron_variant, non_coding_transcript_variant 2
CEP135ENST00000706800.1 linkuse as main transcriptn.645+1257C>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.127
AC:
19275
AN:
151978
Hom.:
1530
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.140
Gnomad AMI
AF:
0.0780
Gnomad AMR
AF:
0.245
Gnomad ASJ
AF:
0.189
Gnomad EAS
AF:
0.258
Gnomad SAS
AF:
0.184
Gnomad FIN
AF:
0.0636
Gnomad MID
AF:
0.0981
Gnomad NFE
AF:
0.0855
Gnomad OTH
AF:
0.133
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.127
AC:
19298
AN:
152096
Hom.:
1536
Cov.:
32
AF XY:
0.131
AC XY:
9720
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.140
Gnomad4 AMR
AF:
0.246
Gnomad4 ASJ
AF:
0.189
Gnomad4 EAS
AF:
0.257
Gnomad4 SAS
AF:
0.184
Gnomad4 FIN
AF:
0.0636
Gnomad4 NFE
AF:
0.0855
Gnomad4 OTH
AF:
0.135
Alfa
AF:
0.104
Hom.:
2127
Bravo
AF:
0.140
Asia WGS
AF:
0.262
AC:
912
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
1.0
DANN
Benign
0.40

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.

Other links and lift over

dbSNP: rs4865047; hg19: chr4-56821806; API