rs2214600

Variant names:

• chrX-24642466-T-A
• rs2214600
• NM_004845.5:c.117+4523A>T

Your query was ambiguous. Multiple possible variants found:

• chrX-24642466-T-A
• chrX-24642466-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_004845.5(PCYT1B):​c.117+4523A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 24)
• Consequence: PCYT1B NM_004845.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.710
• Publications: 0 publications found

Genes affected

PCYT1B (HGNC:8755): (phosphate cytidylyltransferase 1B, choline) The protein encoded by this gene belongs to the cytidylyltransferase family. It is involved in the regulation of phosphatidylcholine biosynthesis. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004845.5. 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
	PCYT1B	NM_004845.5	MANE Select	c.117+4523A>T		intron	N/A	NP_004836.2
	PCYT1B	NM_001163264.2		c.64-23382A>T		intron	N/A	NP_001156736.1	Q9Y5K3-4
	PCYT1B	NM_001163265.2		c.117+4523A>T		intron	N/A	NP_001156737.1	Q9Y5K3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCYT1B	ENST00000379144.7	TSL:1 MANE Select	c.117+4523A>T		intron	N/A	ENSP00000368439.2	Q9Y5K3-1
	PCYT1B	ENST00000379145.5	TSL:1	c.64-23382A>T		intron	N/A	ENSP00000368440.1	Q9Y5K3-4
	PCYT1B	ENST00000356768.8	TSL:1	c.117+4523A>T		intron	N/A	ENSP00000349211.4	Q9Y5K3-2

Frequencies

GnomAD3 genomes Cov.: 24

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

GnomAD4 genome Cov.: 24

Alfa AF: 0.00 Hom.: 5496

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.43
PhyloP100		-0.71

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: rs2214600; hg19: chrX-24660583;