5-75510279-C-T

Variant names:

• chr5-75510279-C-T
• rs5744533
• NM_001379029.1:c.96+833G>A

Variant summary

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

The NM_001379029.1(CERT1):​c.96+833G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 151,850 control chromosomes in the GnomAD database, including 4,312 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 0.23 (4312 hom., cov: 31)
• Consequence: CERT1 NM_001379029.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CERT1	NM_001379029.1	c.96+833G>A		intron_variant	Intron 1 of 16	ENST00000643780.2	NP_001365958.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CERT1	ENST00000643780.2	c.96+833G>A		intron_variant	Intron 1 of 16		NM_001379029.1	ENSP00000495760.1

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35520 AN: 151732 Hom.: 4302 Cov.: 31

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.234 AC: 35559 AN: 151850 Hom.: 4312 Cov.: 31 AF XY: 0.240 AC XY: 17776 AN XY: 74196

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.223

Alfa AF: 0.156 Hom.: 436

Bravo AF: 0.226

Asia WGS AF: 0.357 AC: 1240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.28
DANN	Benign	0.74

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: rs5744533; hg19: chr5-74806104; COSMIC: COSV54039658; COSMIC: COSV54039658;