chr12-101699976-G-A

Variant names:

• chr12-101699976-G-A
• rs1124605
• NM_020244.3:c.273+1842G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020244.3(CHPT1):​c.273+1842G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 152,126 control chromosomes in the GnomAD database, including 49,708 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 0.81 (49708 hom., cov: 32)
• Consequence: CHPT1 NM_020244.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.453
• Publications: 11 publications found

Genes affected

CHPT1 (HGNC:17852): (choline phosphotransferase 1) Enables diacylglycerol cholinephosphotransferase activity. Involved in phosphatidylcholine biosynthetic process and platelet activating factor biosynthetic process. Predicted to be located in Golgi membrane. Predicted to be active in Golgi apparatus and endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020244.3. 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
	CHPT1	NM_020244.3	MANE Select	c.273+1842G>A		intron	N/A	NP_064629.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHPT1	ENST00000229266.8	TSL:1 MANE Select	c.273+1842G>A		intron	N/A	ENSP00000229266.3
	CHPT1	ENST00000552215.5	TSL:1	n.168+1842G>A		intron	N/A	ENSP00000448831.1
	CHPT1	ENST00000549872.5	TSL:5	c.273+1842G>A		intron	N/A	ENSP00000448766.1

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122450 AN: 152008 Hom.: 49646 Cov.: 32

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.807

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.848

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.806 AC: 122568 AN: 152126 Hom.: 49708 Cov.: 32 AF XY: 0.804 AC XY: 59809 AN XY: 74362

African (AFR) AF: 0.904 AC: 37522 AN: 41520

American (AMR) AF: 0.805 AC: 12308 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.807 AC: 2802 AN: 3470

East Asian (EAS) AF: 0.767 AC: 3972 AN: 5178

South Asian (SAS) AF: 0.847 AC: 4085 AN: 4824

European-Finnish (FIN) AF: 0.707 AC: 7462 AN: 10548

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.762 AC: 51775 AN: 67990

Other (OTH) AF: 0.797 AC: 1681 AN: 2110

Alfa AF: 0.775 Hom.: 174362

Bravo AF: 0.815

Asia WGS AF: 0.807 AC: 2804 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.6
DANN	Benign	0.61
PhyloP100		0.45
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: rs1124605; hg19: chr12-102093754;