rs3827608

Positions:

• chr5-75391764-T-C
• chr5-75391764-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001379029.1(CERT1):​c.1189-2077A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0783 in 152,262 control chromosomes in the GnomAD database, including 562 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.078 (562 hom., cov: 32)
• Consequence: CERT1 NM_001379029.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CERT1	NM_001379029.1	c.1189-2077A>G		intron_variant		ENST00000643780.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CERT1	ENST00000643780.2	c.1189-2077A>G		intron_variant			NM_001379029.1	P3

Frequencies

GnomAD3 genomes AF: 0.0782 AC: 11903 AN: 152144 Hom.: 558 Cov.: 32

Gnomad AFR AF: 0.0603

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0682

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.0708

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.0681

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0837

Gnomad OTH AF: 0.0885

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0783 AC: 11919 AN: 152262 Hom.: 562 Cov.: 32 AF XY: 0.0798 AC XY: 5944 AN XY: 74444

Gnomad4 AFR AF: 0.0604

Gnomad4 AMR AF: 0.0682

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.0706

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.0681

Gnomad4 NFE AF: 0.0837

Gnomad4 OTH AF: 0.0866

Alfa AF: 0.0773 Hom.: 50

Bravo AF: 0.0749

Asia WGS AF: 0.117 AC: 405 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.2
DANN	Benign	0.75

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

Other links and lift over

dbSNP: rs3827608; hg19: chr5-74687589;