chr12-101717395-G-C

Position:

• chr12-101717395-G-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CHPT1	NM_020244.3	c.648+583G>C		intron_variant		ENST00000229266.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHPT1	ENST00000229266.8	c.648+583G>C		intron_variant		1	NM_020244.3	P1

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

Gnomad4 AFR exome AF: 0.737

Gnomad4 AMR exome AF: 0.591

Gnomad4 ASJ exome AF: 0.565

Gnomad4 EAS exome AF: 0.905

Gnomad4 SAS exome AF: 0.624

Gnomad4 FIN exome AF: 0.584

Gnomad4 NFE exome AF: 0.536

Gnomad4 OTH exome AF: 0.594

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

Gnomad4 AFR AF: 0.725

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.897

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.614

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1544921; hg19: chr12-102111173;