rs749454395

Variant names:

• chr5-75374198-GAAAAAA-G
• rs749454395
• ENST00000261415.12:c.*9+5133_*9+5138delTTTTTT

Your query was ambiguous. Multiple possible variants found:

• chr5-75374198-GAAAAAA-G
• chr5-75374198-GAAAAAA-GAA
• chr5-75374198-GAAAAAA-GAAA
• chr5-75374198-GAAAAAA-GAAAA
• chr5-75374198-GAAAAAA-GAAAAA
• chr5-75374198-GAAAAAA-GAAAAAAA
• chr5-75374198-GAAAAAA-GAAAAAAAA
• chr5-75374198-GAAAAAA-GAAAAAAAAA
• chr5-75374198-GAAAAAA-GAAAAAAAAAAA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001130105.1(CERT1):​c.*10-13_*10-8delTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000309 in 304,020 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00013 (0 hom., cov: 29)
  • Exomes 𝑓: 0.00038 (0 hom.)
• Consequence: CERT1 NM_001130105.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.975

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 Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAd4 at 11 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CERT1	NM_001130105.1	c.*10-13_*10-8delTTTTTT		splice_region_variant, intron_variant	Intron 18 of 18		NP_001123577.1
CERT1	NM_001379002.1	c.*9+5133_*9+5138delTTTTTT		intron_variant	Intron 17 of 17		NP_001365931.1
CERT1	NM_005713.3	c.*10-13_*10-8delTTTTTT		splice_region_variant, intron_variant	Intron 17 of 17		NP_005704.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CERT1	ENST00000261415.12	c.*9+5133_*9+5138delTTTTTT		intron_variant	Intron 17 of 17	1		ENSP00000261415.8
CERT1	ENST00000405807.10	c.*10-13_*10-8delTTTTTT		splice_region_variant, intron_variant	Intron 18 of 18	5		ENSP00000383996.4
CERT1	ENST00000644072.2	c.*10-13_*10-8delTTTTTT		splice_region_variant, intron_variant	Intron 17 of 17			ENSP00000494110.2

Frequencies

GnomAD3 genomes AF: 0.000130 AC: 11 AN: 84604 Hom.: 0 Cov.: 29

Gnomad AFR AF: 0.000408

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000138

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000378 AC: 83 AN: 219416 Hom.: 0 AF XY: 0.000483 AC XY: 54 AN XY: 111720

Gnomad4 AFR exome AF: 0.000471

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.000726

Gnomad4 EAS exome AF: 0.000194

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.000291

Gnomad4 NFE exome AF: 0.000408

Gnomad4 OTH exome AF: 0.000482

GnomAD4 genome AF: 0.000130 AC: 11 AN: 84604 Hom.: 0 Cov.: 29 AF XY: 0.000125 AC XY: 5 AN XY: 39978

Gnomad4 AFR AF: 0.000408

Gnomad4 AMR AF: 0.000138

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs749454395; hg19: chr5-74670023;