1-111155726-T-C

Position:

• chr1-111155726-T-C

Variant summary

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

The NM_006090.5(CEPT1):​c.340-3654T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 151,888 control chromosomes in the GnomAD database, including 37,763 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 0.70 (37763 hom., cov: 30)
• Consequence: CEPT1 NM_006090.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.89

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]

CEPT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEPT1	NM_006090.5	c.340-3654T>C		intron_variant		ENST00000357172.9	NP_006081.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEPT1	ENST00000357172.9	c.340-3654T>C		intron_variant		1	NM_006090.5	ENSP00000349696.4

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106200 AN: 151768 Hom.: 37698 Cov.: 30

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.700 AC: 106324 AN: 151888 Hom.: 37763 Cov.: 30 AF XY: 0.700 AC XY: 51983 AN XY: 74238

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.674

Alfa AF: 0.690 Hom.: 4572

Bravo AF: 0.695

Asia WGS AF: 0.744 AC: 2588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.16

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: rs325927; hg19: chr1-111698348;