NM_006090.5:c.340-3654T>C

Variant names:

• chr1-111155726-T-C
• rs325927
• NM_006090.5:c.340-3654T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006090.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEPT1	NM_006090.5	MANE Select	c.340-3654T>C		intron	N/A	NP_006081.1
	CEPT1	NM_001007794.3		c.340-3654T>C		intron	N/A	NP_001007795.1
	CEPT1	NM_001330743.2		c.340-3654T>C		intron	N/A	NP_001317672.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEPT1	ENST00000357172.9	TSL:1 MANE Select	c.340-3654T>C		intron	N/A	ENSP00000349696.4
	CEPT1	ENST00000545121.5	TSL:1	c.340-3654T>C		intron	N/A	ENSP00000441980.1
	CEPT1	ENST00000498239.5	TSL:1	n.548-3654T>C		intron	N/A

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

African (AFR) AF: 0.824 AC: 34143 AN: 41434

American (AMR) AF: 0.628 AC: 9581 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1989 AN: 3464

East Asian (EAS) AF: 0.625 AC: 3213 AN: 5142

South Asian (SAS) AF: 0.767 AC: 3689 AN: 4810

European-Finnish (FIN) AF: 0.689 AC: 7270 AN: 10552

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.654 AC: 44432 AN: 67908

Other (OTH) AF: 0.674 AC: 1420 AN: 2106

Alfa AF: 0.694 Hom.: 4815

Bravo AF: 0.695

Asia WGS AF: 0.744 AC: 2588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.16
PhyloP100		-2.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs325927; hg19: chr1-111698348;