12-101707848-C-T

Variant names:

• chr12-101707848-C-T
• rs7980436
• NM_020244.3:c.274-6242C>T

Variant summary

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

The NM_020244.3(CHPT1):​c.274-6242C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,102 control chromosomes in the GnomAD database, including 1,829 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 0.14 (1829 hom., cov: 31)
• Consequence: CHPT1 NM_020244.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHPT1	NM_020244.3	c.274-6242C>T		intron_variant	Intron 1 of 8	ENST00000229266.8	NP_064629.2
CHPT1	XM_011538574.2	c.274-6242C>T		intron_variant	Intron 1 of 7		XP_011536876.1
CHPT1	XR_001748818.2	n.496-6242C>T		intron_variant	Intron 1 of 7
CHPT1	XR_245946.3	n.496-6242C>T		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHPT1	ENST00000229266.8	c.274-6242C>T		intron_variant	Intron 1 of 8	1	NM_020244.3	ENSP00000229266.3

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20976 AN: 151982 Hom.: 1830 Cov.: 31

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0785

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0904

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.138 AC: 20996 AN: 152102 Hom.: 1829 Cov.: 31 AF XY: 0.139 AC XY: 10331 AN XY: 74352

African (AFR) AF: 0.247 AC: 10219 AN: 41448

American (AMR) AF: 0.0783 AC: 1197 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 386 AN: 3472

East Asian (EAS) AF: 0.120 AC: 623 AN: 5180

South Asian (SAS) AF: 0.198 AC: 955 AN: 4814

European-Finnish (FIN) AF: 0.100 AC: 1061 AN: 10588

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0904 AC: 6148 AN: 68006

Other (OTH) AF: 0.125 AC: 264 AN: 2114

Alfa AF: 0.105 Hom.: 1663

Bravo AF: 0.138

Asia WGS AF: 0.184 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.46
DANN	Benign	0.45
PhyloP100		-0.48
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs7980436; hg19: chr12-102101626;