rs1124605

Positions:

• chr12-101699976-G-A
• chr12-101699976-G-C
• chr12-101699976-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000229266.8(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 ENST00000229266.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.453

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHPT1	NM_020244.3	c.273+1842G>A		intron_variant		ENST00000229266.8	NP_064629.2
CHPT1	XM_011538574.2	c.273+1842G>A		intron_variant			XP_011536876.1
CHPT1	XR_001748818.2	n.495+1842G>A		intron_variant, non_coding_transcript_variant
CHPT1	XR_245946.3	n.495+1842G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHPT1	ENST00000229266.8	c.273+1842G>A		intron_variant		1	NM_020244.3	ENSP00000229266	P1

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

Gnomad4 AFR AF: 0.904

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.807

Gnomad4 EAS AF: 0.767

Gnomad4 SAS AF: 0.847

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.797

Alfa AF: 0.770 Hom.: 70716

Bravo AF: 0.815

Asia WGS AF: 0.807 AC: 2804 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.6
DANN	Benign	0.61

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

Publications

LitVar

Other links and lift over

dbSNP: rs1124605; hg19: chr12-102093754;