5-75374179-C-T
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_001379004.1(CERT1):c.1682G>A(p.Arg561Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000627 in 398,510 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000089 ( 0 hom., cov: 29)
Exomes 𝑓: 0.000048 ( 0 hom. )
Consequence
CERT1
NM_001379004.1 missense
NM_001379004.1 missense
Scores
1
5
Clinical Significance
Conservation
PhyloP100: 4.06
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.17406648).
BP6
Variant 5-75374179-C-T is Benign according to our data. Variant chr5-75374179-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3389224.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 13 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CERT1 | NM_001379004.1 | c.1682G>A | p.Arg561Lys | missense_variant | 16/16 | NP_001365933.1 | ||
CERT1 | XM_011543090.4 | c.1760G>A | p.Arg587Lys | missense_variant | 17/17 | XP_011541392.1 | ||
CERT1 | NM_001130105.1 | c.*22G>A | 3_prime_UTR_variant | 19/19 | NP_001123577.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CERT1 | ENST00000261415.12 | c.*9+5158G>A | intron_variant | 1 | ENSP00000261415.8 | |||||
CERT1 | ENST00000642556.1 | c.1682G>A | p.Arg561Lys | missense_variant | 16/16 | ENSP00000496016.1 | ||||
CERT1 | ENST00000405807.10 | c.*22G>A | 3_prime_UTR_variant | 19/19 | 5 | ENSP00000383996.4 |
Frequencies
GnomAD3 genomes AF: 0.0000890 AC: 13AN: 145996Hom.: 0 Cov.: 29
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GnomAD4 exome AF: 0.0000475 AC: 12AN: 252480Hom.: 0 Cov.: 0 AF XY: 0.0000546 AC XY: 7AN XY: 128250
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GnomAD4 genome AF: 0.0000890 AC: 13AN: 146030Hom.: 0 Cov.: 29 AF XY: 0.000113 AC XY: 8AN XY: 70802
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2024 | CERT1: BS1 - |
Computational scores
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BayesDel_noAF
Benign
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Benign
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D
LIST_S2
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at