5-75374136-C-CT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PVS1_ModerateBP6_ModerateBS2

The NM_001379004.1(CERT1):​c.1724dupA​(p.Leu576AlafsTer26) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00795 in 324,058 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0034 ( 1 hom., cov: 31)
Exomes 𝑓: 0.011 ( 2 hom. )

Consequence

CERT1
NM_001379004.1 frameshift

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.786
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.0517 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
BP6
Variant 5-75374136-C-CT is Benign according to our data. Variant chr5-75374136-C-CT is described in ClinVar as [Likely_benign]. Clinvar id is 2673015.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 467 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CERT1NM_001379004.1 linkc.1724dupA p.Leu576AlafsTer26 frameshift_variant Exon 16 of 16 NP_001365933.1
CERT1XM_011543090.4 linkc.1802dupA p.Leu602AlafsTer26 frameshift_variant Exon 17 of 17 XP_011541392.1
CERT1NM_001130105.1 linkc.*64dupA 3_prime_UTR_variant Exon 19 of 19 NP_001123577.1 Q9Y5P4-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CERT1ENST00000261415.12 linkc.*9+5200dupA intron_variant Intron 17 of 17 1 ENSP00000261415.8 Q9Y5P4-1
CERT1ENST00000642556.1 linkc.1724dupA p.Leu576AlafsTer26 frameshift_variant Exon 16 of 16 ENSP00000496016.1 A0A2R8Y7C5
CERT1ENST00000644072 linkc.*64dupA 3_prime_UTR_variant Exon 18 of 18 ENSP00000494110.2 Q9Y5P4-1

Frequencies

GnomAD3 genomes
AF:
0.00337
AC:
466
AN:
138444
Hom.:
1
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.000696
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000984
Gnomad ASJ
AF:
0.00687
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000455
Gnomad FIN
AF:
0.00865
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00513
Gnomad OTH
AF:
0.00162
GnomAD4 exome
AF:
0.0114
AC:
2108
AN:
185576
Hom.:
2
Cov.:
0
AF XY:
0.0113
AC XY:
1068
AN XY:
94444
show subpopulations
Gnomad4 AFR exome
AF:
0.00712
Gnomad4 AMR exome
AF:
0.00622
Gnomad4 ASJ exome
AF:
0.0106
Gnomad4 EAS exome
AF:
0.00443
Gnomad4 SAS exome
AF:
0.00681
Gnomad4 FIN exome
AF:
0.0206
Gnomad4 NFE exome
AF:
0.0120
Gnomad4 OTH exome
AF:
0.00937
GnomAD4 genome
AF:
0.00337
AC:
467
AN:
138482
Hom.:
1
Cov.:
31
AF XY:
0.00348
AC XY:
232
AN XY:
66638
show subpopulations
Gnomad4 AFR
AF:
0.000721
Gnomad4 AMR
AF:
0.000983
Gnomad4 ASJ
AF:
0.00687
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000457
Gnomad4 FIN
AF:
0.00865
Gnomad4 NFE
AF:
0.00513
Gnomad4 OTH
AF:
0.00161
Asia WGS
AF:
0.00982
AC:
34
AN:
3478

ClinVar

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

Submissions by phenotype

not provided Benign:1
Apr 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

CERT1: BS1 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs545323650; hg19: chr5-74669961; API