12-101717395-G-C

Variant names:

• chr12-101717395-G-C
• rs1544921
• NM_020244.3:c.648+583G>C

Variant summary

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

The NM_020244.3(CHPT1):​c.648+583G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 428,448 control chromosomes in the GnomAD database, including 77,455 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 0.61 (29282 hom., cov: 30)
  • Exomes 𝑓: 0.58 (48173 hom.)
• Consequence: CHPT1 NM_020244.3 intron
• Scores: Splicing: ADA: 0.00001899
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.832
• Publications: 7 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHPT1	NM_020244.3	c.648+583G>C		intron_variant	Intron 4 of 8	ENST00000229266.8	NP_064629.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHPT1	ENST00000229266.8	c.648+583G>C		intron_variant	Intron 4 of 8	1	NM_020244.3	ENSP00000229266.3

Frequencies

GnomAD3 genomes AF: 0.613 AC: 92967 AN: 151672 Hom.: 29250 Cov.: 30

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.609

GnomAD4 exome AF: 0.583 AC: 161200 AN: 276658 Hom.: 48173 Cov.: 0 AF XY: 0.585 AC XY: 92518 AN XY: 158096

African (AFR) AF: 0.737 AC: 5828 AN: 7906

American (AMR) AF: 0.591 AC: 14664 AN: 24798

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 5568 AN: 9852

East Asian (EAS) AF: 0.905 AC: 8103 AN: 8954

South Asian (SAS) AF: 0.624 AC: 33987 AN: 54490

European-Finnish (FIN) AF: 0.584 AC: 6522 AN: 11168

Middle Eastern (MID) AF: 0.639 AC: 1706 AN: 2668

European-Non Finnish (NFE) AF: 0.536 AC: 77128 AN: 143872

Other (OTH) AF: 0.594 AC: 7694 AN: 12950

GnomAD4 genome AF: 0.613 AC: 93064 AN: 151790 Hom.: 29282 Cov.: 30 AF XY: 0.616 AC XY: 45694 AN XY: 74170

African (AFR) AF: 0.725 AC: 30016 AN: 41404

American (AMR) AF: 0.562 AC: 8572 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1994 AN: 3462

East Asian (EAS) AF: 0.897 AC: 4638 AN: 5172

South Asian (SAS) AF: 0.647 AC: 3115 AN: 4812

European-Finnish (FIN) AF: 0.605 AC: 6356 AN: 10506

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36326 AN: 67878

Other (OTH) AF: 0.614 AC: 1287 AN: 2096

Alfa AF: 0.442 Hom.: 1195

Bravo AF: 0.617

Asia WGS AF: 0.792 AC: 2750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.5
DANN	Benign	0.58
PhyloP100		-0.83
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000019
dbscSNV1_RF	Benign	0.010
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: rs1544921; hg19: chr12-102111173;