X-24642466-T-C

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_004845.5(PCYT1B):​c.117+4523A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.65 (16879 hom., 21739 hem., cov: 24)
  • Failed GnomAD Quality Control
• 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 -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCYT1B	NM_004845.5	c.117+4523A>G		intron_variant	Intron 1 of 7	ENST00000379144.7	NP_004836.2
PCYT1B	NM_001163264.2	c.64-23382A>G		intron_variant	Intron 1 of 7		NP_001156736.1
PCYT1B	NM_001163265.2	c.117+4523A>G		intron_variant	Intron 1 of 8		NP_001156737.1
PCYT1B	XM_017029977.2	c.-291-2005A>G		intron_variant	Intron 1 of 8		XP_016885466.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCYT1B	ENST00000379144.7	c.117+4523A>G		intron_variant	Intron 1 of 7	1	NM_004845.5	ENSP00000368439.2
PCYT1B	ENST00000379145.5	c.64-23382A>G		intron_variant	Intron 1 of 7	1		ENSP00000368440.1
PCYT1B	ENST00000356768.8	c.117+4523A>G		intron_variant	Intron 1 of 8	1		ENSP00000349211.4
PCYT1B	ENST00000496020.1	n.39+4523A>G		intron_variant	Intron 1 of 6	3		ENSP00000436562.1

Frequencies

GnomAD3 genomes AF: 0.652 AC: 72522 AN: 111294 Hom.: 16879 Cov.: 24

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.542

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.645

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.652 AC: 72566 AN: 111347 Hom.: 16879 Cov.: 24 AF XY: 0.648 AC XY: 21739 AN XY: 33567

African (AFR) AF: 0.779 AC: 23925 AN: 30694

American (AMR) AF: 0.687 AC: 7153 AN: 10410

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1449 AN: 2634

East Asian (EAS) AF: 0.695 AC: 2462 AN: 3541

South Asian (SAS) AF: 0.566 AC: 1519 AN: 2683

European-Finnish (FIN) AF: 0.563 AC: 3366 AN: 5981

Middle Eastern (MID) AF: 0.535 AC: 116 AN: 217

European-Non Finnish (NFE) AF: 0.592 AC: 31344 AN: 52980

Other (OTH) AF: 0.642 AC: 981 AN: 1527

Alfa AF: 0.610 Hom.: 5496

Bravo AF: 0.669

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.56
PhyloP100		-0.71
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: rs2214600; hg19: chrX-24660583;