chr12-101726374-C-T

Variant names:

• chr12-101726374-C-T
• rs116668070
• NM_020244.3:c.1146C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_020244.3(CHPT1):​c.1146C>T​(p.Phe382Phe) variant causes a synonymous change. The variant allele was found at a frequency of 0.00132 in 1,612,924 control chromosomes in the GnomAD database, including 62 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0018 (9 hom., cov: 32)
  • Exomes 𝑓: 0.0013 (53 hom.)
• Consequence: CHPT1 NM_020244.3 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 4.52
• Publications: 2 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 -10 ACMG points.

• BP6: Variant 12-101726374-C-T is Benign according to our data. Variant chr12-101726374-C-T is described in ClinVar as Benign. ClinVar VariationId is 780150.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.00181 (275/152154) while in subpopulation EAS AF = 0.046 (238/5178). AF 95% confidence interval is 0.0412. There are 9 homozygotes in GnomAd4. There are 153 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 9 AR gene

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHPT1	NM_020244.3	MANE Select	c.1146C>T	p.Phe382Phe	synonymous	Exon 8 of 9	NP_064629.2	Q8WUD6-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHPT1	ENST00000229266.8	TSL:1 MANE Select	c.1146C>T	p.Phe382Phe	synonymous	Exon 8 of 9	ENSP00000229266.3	Q8WUD6-1
	CHPT1	ENST00000552215.5	TSL:1	n.*516C>T		non_coding_transcript_exon	Exon 9 of 9	ENSP00000448831.1	H0YI84
	CHPT1	ENST00000552215.5	TSL:1	n.*516C>T		3_prime_UTR	Exon 9 of 9	ENSP00000448831.1	H0YI84

Frequencies

GnomAD3 genomes AF: 0.00180 AC: 274 AN: 152036 Hom.: 9 Cov.: 32

Gnomad AFR AF: 0.0000242

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000525

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.0459

Gnomad SAS AF: 0.00187

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000588

Gnomad OTH AF: 0.00526

GnomAD2 exomes AF: 0.00415 AC: 1042 AN: 250864 AF XY: 0.00381

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000202

Gnomad ASJ exome AF: 0.00149

Gnomad EAS exome AF: 0.0538

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000617

Gnomad OTH exome AF: 0.00229

GnomAD4 exome AF: 0.00127 AC: 1850 AN: 1460770 Hom.: 53 Cov.: 30 AF XY: 0.00116 AC XY: 840 AN XY: 726744

African (AFR) AF: 0.00 AC: 0 AN: 33450

American (AMR) AF: 0.000157 AC: 7 AN: 44718

Ashkenazi Jewish (ASJ) AF: 0.00142 AC: 37 AN: 26118

East Asian (EAS) AF: 0.0356 AC: 1414 AN: 39666

South Asian (SAS) AF: 0.000464 AC: 40 AN: 86214

European-Finnish (FIN) AF: 0.0000188 AC: 1 AN: 53068

Middle Eastern (MID) AF: 0.000347 AC: 2 AN: 5766

European-Non Finnish (NFE) AF: 0.0000288 AC: 32 AN: 1111406

Other (OTH) AF: 0.00525 AC: 317 AN: 60364

GnomAD4 genome AF: 0.00181 AC: 275 AN: 152154 Hom.: 9 Cov.: 32 AF XY: 0.00206 AC XY: 153 AN XY: 74390

African (AFR) AF: 0.0000241 AC: 1 AN: 41526

American (AMR) AF: 0.000524 AC: 8 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.000865 AC: 3 AN: 3470

East Asian (EAS) AF: 0.0460 AC: 238 AN: 5178

South Asian (SAS) AF: 0.00187 AC: 9 AN: 4816

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10590

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000588 AC: 4 AN: 67984

Other (OTH) AF: 0.00568 AC: 12 AN: 2112

Alfa AF: 0.000416 Hom.: 0

Bravo AF: 0.00213

Asia WGS AF: 0.0190 AC: 65 AN: 3478

EpiCase AF: 0.00

EpiControl AF: 0.000178

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	9.5
DANN	Benign	0.81
PhyloP100		4.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=99/1	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.29		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.29		Position offset: 30

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs116668070; hg19: chr12-102120152;