5-75374179-C-T

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

Scores

1
5

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.06
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 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
CERT1NM_001379004.1 linkuse as main transcriptc.1682G>A p.Arg561Lys missense_variant 16/16 NP_001365933.1
CERT1XM_011543090.4 linkuse as main transcriptc.1760G>A p.Arg587Lys missense_variant 17/17 XP_011541392.1
CERT1NM_001130105.1 linkuse as main transcriptc.*22G>A 3_prime_UTR_variant 19/19 NP_001123577.1 Q9Y5P4-3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CERT1ENST00000261415.12 linkuse as main transcriptc.*9+5158G>A intron_variant 1 ENSP00000261415.8 Q9Y5P4-1
CERT1ENST00000642556.1 linkuse as main transcriptc.1682G>A p.Arg561Lys missense_variant 16/16 ENSP00000496016.1 A0A2R8Y7C5
CERT1ENST00000405807.10 linkuse as main transcriptc.*22G>A 3_prime_UTR_variant 19/195 ENSP00000383996.4 Q9Y5P4-3

Frequencies

GnomAD3 genomes
AF:
0.0000890
AC:
13
AN:
145996
Hom.:
0
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.0000508
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000198
Gnomad SAS
AF:
0.00215
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000475
AC:
12
AN:
252480
Hom.:
0
Cov.:
0
AF XY:
0.0000546
AC XY:
7
AN XY:
128250
show subpopulations
Gnomad4 AFR exome
AF:
0.000278
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00252
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000599
GnomAD4 genome
AF:
0.0000890
AC:
13
AN:
146030
Hom.:
0
Cov.:
29
AF XY:
0.000113
AC XY:
8
AN XY:
70802
show subpopulations
Gnomad4 AFR
AF:
0.0000507
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000199
Gnomad4 SAS
AF:
0.00217
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

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 submitterclinical testingCeGaT Center for Human Genetics TuebingenNov 01, 2024CERT1: BS1 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.50
CADD
Uncertain
25
DANN
Benign
0.81
FATHMM_MKL
Uncertain
0.79
D
LIST_S2
Benign
0.15
T
MetaRNN
Benign
0.17
T
GERP RS
5.1

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: rs558900603; hg19: chr5-74670004; API