Variant rs938350 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024419.5(PGS1):c.881-97G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 1,263,102 control chromosomes in the GnomAD database, including 233,608 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 0.61 ( 28348 hom., cov: 31)

Exomes 𝑓: 0.61 ( 205260 hom. )

Consequence

PGS1
NM_024419.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.58

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PGS1	NM_024419.5 linkuse as main transcript	c.881-97G>A		intron_variant		ENST00000262764.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PGS1	ENST00000262764.11 linkuse as main transcript	c.881-97G>A		intron_variant		1	NM_024419.5	P1	Q32NB8-1

Frequencies

GnomAD3 genomes

AF:

0.610

AC:

92631

AN:

151854

Hom.:

28331

Cov.:

show subpopulations

Gnomad AFR

AF:

0.597

Gnomad AMI

AF:

0.669

Gnomad AMR

AF:

0.648

Gnomad ASJ

AF:

0.598

Gnomad EAS

AF:

0.440

Gnomad SAS

AF:

0.570

Gnomad FIN

AF:

0.684

Gnomad MID

AF:

0.636

Gnomad NFE

AF:

0.613

Gnomad OTH

AF:

0.628

GnomAD4 exome

AF:

0.606

AC:

673213

AN:

1111130

Hom.:

205260

AF XY:

0.604

AC XY:

336092

AN XY:

556288

show subpopulations

Gnomad4 AFR exome

AF:

0.604

Gnomad4 AMR exome

AF:

0.665

Gnomad4 ASJ exome

AF:

0.599

Gnomad4 EAS exome

AF:

0.441

Gnomad4 SAS exome

AF:

0.570

Gnomad4 FIN exome

AF:

0.678

Gnomad4 NFE exome

AF:

0.609

Gnomad4 OTH exome

AF:

0.615

GnomAD4 genome

AF:

0.610

AC:

92687

AN:

151972

Hom.:

28348

Cov.:

AF XY:

0.611

AC XY:

45391

AN XY:

74274

show subpopulations

Gnomad4 AFR

AF:

0.597

Gnomad4 AMR

AF:

0.648

Gnomad4 ASJ

AF:

0.598

Gnomad4 EAS

AF:

0.441

Gnomad4 SAS

AF:

0.571

Gnomad4 FIN

AF:

0.684

Gnomad4 NFE

AF:

0.613

Gnomad4 OTH

AF:

0.624

Alfa

AF:

0.624

Hom.:

5810

Bravo

AF:

0.602

Asia WGS

AF:

0.553

AC:

1922

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.0020

DANN

Benign

0.66

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over