GeneBe

rs749454395

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001130105.1(CERT1):​c.*10-15_*10-8delTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000091 in 219,868 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 29)
Exomes 𝑓: 0.0000091 ( 0 hom. )

Consequence

CERT1
NM_001130105.1 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.975

Publications

0 publications found
Variant links:
Genes affected
CERT1 (HGNC:2205): (ceramide transporter 1) This gene encodes a kinase that specifically phosphorylates the N-terminal region of the non-collagenous domain of the alpha 3 chain of type IV collagen, known as the Goodpasture antigen. Goodpasture disease is the result of an autoimmune response directed at this antigen. One isoform of this protein is also involved in ceramide intracellular transport. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
CERT1 Gene-Disease associations (from GenCC):
  • intellectual disability, autosomal dominant 34
    Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001130105.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
CERT1
NM_001130105.1
c.*10-15_*10-8delTTTTTTTT
splice_region intron
N/ANP_001123577.1Q9Y5P4-3
CERT1
NM_001379002.1
c.*9+5131_*9+5138delTTTTTTTT
intron
N/ANP_001365931.1Q9Y5P4-1
CERT1
NM_005713.3
c.*10-15_*10-8delTTTTTTTT
splice_region intron
N/ANP_005704.1Q9Y5P4-1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
CERT1
ENST00000261415.12
TSL:1
c.*9+5131_*9+5138delTTTTTTTT
intron
N/AENSP00000261415.8Q9Y5P4-1
CERT1
ENST00000405807.10
TSL:5
c.*10-15_*10-8delTTTTTTTT
splice_region intron
N/AENSP00000383996.4Q9Y5P4-3
CERT1
ENST00000957920.1
c.*10-15_*10-8delTTTTTTTT
splice_region intron
N/AENSP00000627979.1

Frequencies

GnomAD3 genomes
Cov.:
29
GnomAD4 exome
AF:
0.00000910
AC:
2
AN:
219868
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
111970
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
6372
American (AMR)
AF:
0.00
AC:
0
AN:
6668
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
8284
East Asian (EAS)
AF:
0.00
AC:
0
AN:
20672
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2482
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
17210
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
1152
European-Non Finnish (NFE)
AF:
0.0000140
AC:
2
AN:
142476
Other (OTH)
AF:
0.00
AC:
0
AN:
14552
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.450
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.97

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs749454395; hg19: chr5-74670023; API