rs1335645

Positions:

• chr1-111141654-A-G
• chr1-111141654-A-T

Variant summary

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

The NM_006090.5(CEPT1):​c.-74+1347A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,004 control chromosomes in the GnomAD database, including 1,983 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 0.15 (1983 hom., cov: 32)
• Consequence: CEPT1 NM_006090.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116

Genes affected

CEPT1 (HGNC:24289): (choline/ethanolamine phosphotransferase 1) This gene codes for a choline/ethanolaminephosphotransferase, which functions in the synthesis of choline- or ethanolamine- containing phospholipids. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEPT1	NM_006090.5	c.-74+1347A>G		intron_variant		ENST00000357172.9	NP_006081.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEPT1	ENST00000357172.9	c.-74+1347A>G		intron_variant		1	NM_006090.5	ENSP00000349696	P4

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22341 AN: 151888 Hom.: 1978 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.0993

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.147 AC: 22372 AN: 152004 Hom.: 1983 Cov.: 32 AF XY: 0.150 AC XY: 11160 AN XY: 74304

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.0993

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.145

Alfa AF: 0.110 Hom.: 964

Bravo AF: 0.154

Asia WGS AF: 0.239 AC: 837 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.48

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: rs1335645; hg19: chr1-111684276;