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GeneBe

11-101958339-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2

The NM_020802.4(CEP126):c.678C>T(p.Leu226=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00175 in 1,613,704 control chromosomes in the GnomAD database, including 47 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0096 ( 27 hom., cov: 32)
Exomes 𝑓: 0.00093 ( 20 hom. )

Consequence

CEP126
NM_020802.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.226
Variant links:
Genes affected
CEP126 (HGNC:29264): (centrosomal protein 126) Involved in cilium assembly; cytoplasmic microtubule organization; and mitotic spindle organization. Located in centrosome; ciliary base; and midbody. [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 -13 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=-0.31).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-101958339-C-T is Benign according to our data. Variant chr11-101958339-C-T is described in ClinVar as [Benign]. Clinvar id is 786211.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=0.226 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00962 (1464/152224) while in subpopulation AFR AF= 0.0338 (1403/41542). AF 95% confidence interval is 0.0323. There are 27 homozygotes in gnomad4. There are 715 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
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 25 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CEP126NM_020802.4 linkuse as main transcriptc.678C>T p.Leu226= synonymous_variant 5/11 ENST00000263468.13
CEP126NM_001363543.2 linkuse as main transcriptc.81C>T p.Leu27= synonymous_variant 6/12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CEP126ENST00000263468.13 linkuse as main transcriptc.678C>T p.Leu226= synonymous_variant 5/111 NM_020802.4 P1
CEP126ENST00000532529.1 linkuse as main transcriptc.*174C>T 3_prime_UTR_variant, NMD_transcript_variant 4/105
CEP126ENST00000670091.1 linkuse as main transcriptc.*721C>T 3_prime_UTR_variant, NMD_transcript_variant 6/12
CEP126ENST00000670318.1 linkuse as main transcriptc.*190C>T 3_prime_UTR_variant, NMD_transcript_variant 6/12

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00955
AC:
1452
AN:
152106
Hom.:
25
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0336
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00242
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000147
Gnomad OTH
AF:
0.00528
GnomAD3 exomes
AF:
0.00233
AC:
584
AN:
250866
Hom.:
9
AF XY:
0.00174
AC XY:
236
AN XY:
135674
show subpopulations
Gnomad AFR exome
AF:
0.0331
Gnomad AMR exome
AF:
0.000955
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000123
Gnomad OTH exome
AF:
0.000491
GnomAD4 exome
AF:
0.000928
AC:
1356
AN:
1461480
Hom.:
20
Cov.:
31
AF XY:
0.000779
AC XY:
566
AN XY:
727024
show subpopulations
Gnomad4 AFR exome
AF:
0.0327
Gnomad4 AMR exome
AF:
0.00139
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000580
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000630
Gnomad4 OTH exome
AF:
0.00200
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00962
AC:
1464
AN:
152224
Hom.:
27
Cov.:
32
AF XY:
0.00961
AC XY:
715
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.0338
Gnomad4 AMR
AF:
0.00242
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000415
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000147
Gnomad4 OTH
AF:
0.00523
Alfa
AF:
0.00270
Hom.:
2
Bravo
AF:
0.0104
Asia WGS
AF:
0.00115
AC:
4
AN:
3478
EpiCase
AF:
0.0000545
EpiControl
AF:
0.000119

ClinVar

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

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 04, 2017- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.31
Cadd
Benign
6.8
Dann
Benign
0.67

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: rs61742070; hg19: chr11-101829070; API