chr17-78407903-G-A

Position:

• chr17-78407903-G-A

Variant summary

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

The NM_024419.5(PGS1):​c.1402+3814G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 152,086 control chromosomes in the GnomAD database, including 16,659 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 0.46 (16659 hom., cov: 33)
• Consequence: PGS1 NM_024419.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259

Genes affected

PGS1 (HGNC:30029): (phosphatidylglycerophosphate synthase 1) Predicted to enable CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity and calcium ion binding activity. Predicted to be involved in cardiolipin biosynthetic process and diacylglycerol metabolic process. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

PGS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PGS1	NM_024419.5	c.1402+3814G>A		intron_variant		ENST00000262764.11	NP_077733.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PGS1	ENST00000262764.11	c.1402+3814G>A		intron_variant		1	NM_024419.5	ENSP00000262764.5

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70003 AN: 151968 Hom.: 16654 Cov.: 33

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.460 AC: 70018 AN: 152086 Hom.: 16659 Cov.: 33 AF XY: 0.466 AC XY: 34667 AN XY: 74340

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.475

Alfa AF: 0.472 Hom.: 25348

Bravo AF: 0.446

Asia WGS AF: 0.423 AC: 1470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.2
DANN	Benign	0.67

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: rs4129767; hg19: chr17-76403984;