NM_006090.5:c.-74+1347A>G

Variant names:

• chr1-111141654-A-G
• rs1335645
• NM_006090.5:c.-74+1347A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.267 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.-74+1347A>G		intron	N/A	NP_006081.1
	CEPT1	NM_001007794.3		c.-74+1893A>G		intron	N/A	NP_001007795.1
	CEPT1	NM_001330743.2		c.-74+1740A>G		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.-74+1347A>G		intron	N/A	ENSP00000349696.4
	CEPT1	ENST00000545121.5	TSL:1	c.-74+1893A>G		intron	N/A	ENSP00000441980.1
	CEPT1	ENST00000498239.5	TSL:1	n.135+1893A>G		intron	N/A

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

African (AFR) AF: 0.214 AC: 8862 AN: 41392

American (AMR) AF: 0.176 AC: 2689 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0993 AC: 344 AN: 3464

East Asian (EAS) AF: 0.116 AC: 602 AN: 5182

South Asian (SAS) AF: 0.280 AC: 1348 AN: 4822

European-Finnish (FIN) AF: 0.101 AC: 1070 AN: 10574

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7051 AN: 67978

Other (OTH) AF: 0.145 AC: 306 AN: 2108

Alfa AF: 0.117 Hom.: 3550

Bravo AF: 0.154

Asia WGS AF: 0.239 AC: 837 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.48
PhyloP100		-0.12
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: rs1335645; hg19: chr1-111684276;