Variant chr9-78297199-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_058179.4(PSAT1):c.-12G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 1,593,282 control chromosomes in the GnomAD database, including 486,704 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.79 ( 48248 hom., cov: 34)

Exomes 𝑓: 0.78 ( 438456 hom. )

Consequence

PSAT1
NM_058179.4 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -1.48

Variant links:

Genes affected

PSAT1 (HGNC:19129): (phosphoserine aminotransferase 1) This gene encodes a member of the class-V pyridoxal-phosphate-dependent aminotransferase family. The encoded protein is a phosphoserine aminotransferase and decreased expression may be associated with schizophrenia. Mutations in this gene are also associated with phosphoserine aminotransferase deficiency. Alternative splicing results in multiple transcript variants. Pseudogenes of this gene have been defined on chromosomes 1, 3, and 8. [provided by RefSeq, Jul 2013]

PSAT1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 9-78297199-G-C is Benign according to our data. Variant chr9-78297199-G-C is described in ClinVar as [Benign]. Clinvar id is 367450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-78297199-G-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSAT1	NM_058179.4 linkuse as main transcript	c.-12G>C		5_prime_UTR_variant	1/9	ENST00000376588.4	NP_478059.1
PSAT1	NM_021154.5 linkuse as main transcript	c.-12G>C		5_prime_UTR_variant	1/8		NP_066977.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSAT1	ENST00000376588.4 linkuse as main transcript	c.-12G>C		5_prime_UTR_variant	1/9	1	NM_058179.4	ENSP00000365773	P1	Q9Y617-1
PSAT1	ENST00000347159.6 linkuse as main transcript	c.-12G>C		5_prime_UTR_variant	1/8	1		ENSP00000317606		Q9Y617-2

Frequencies

GnomAD3 genomes

AF:

0.795

AC:

120866

AN:

152086

Hom.:

48212

Cov.:

show subpopulations

Gnomad AFR

AF:

0.818

Gnomad AMI

AF:

0.709

Gnomad AMR

AF:

0.831

Gnomad ASJ

AF:

0.782

Gnomad EAS

AF:

0.674

Gnomad SAS

AF:

0.719

Gnomad FIN

AF:

0.811

Gnomad MID

AF:

0.785

Gnomad NFE

AF:

0.786

Gnomad OTH

AF:

0.786

GnomAD3 exomes

AF:

0.785

AC:

169160

AN:

215464

Hom.:

66798

AF XY:

0.779

AC XY:

91924

AN XY:

117966

show subpopulations

Gnomad AFR exome

AF:

0.822

Gnomad AMR exome

AF:

0.881

Gnomad ASJ exome

AF:

0.774

Gnomad EAS exome

AF:

0.675

Gnomad SAS exome

AF:

0.728

Gnomad FIN exome

AF:

0.801

Gnomad NFE exome

AF:

0.782

Gnomad OTH exome

AF:

0.789

GnomAD4 exome

AF:

0.779

AC:

1122336

AN:

1441078

Hom.:

438456

Cov.:

AF XY:

0.777

AC XY:

556246

AN XY:

716034

show subpopulations

Gnomad4 AFR exome

AF:

0.813

Gnomad4 AMR exome

AF:

0.874

Gnomad4 ASJ exome

AF:

0.781

Gnomad4 EAS exome

AF:

0.613

Gnomad4 SAS exome

AF:

0.731

Gnomad4 FIN exome

AF:

0.803

Gnomad4 NFE exome

AF:

0.783

Gnomad4 OTH exome

AF:

0.773

GnomAD4 genome

AF:

0.795

AC:

120958

AN:

152204

Hom.:

48248

Cov.:

AF XY:

0.795

AC XY:

59181

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.818

Gnomad4 AMR

AF:

0.831

Gnomad4 ASJ

AF:

0.782

Gnomad4 EAS

AF:

0.673

Gnomad4 SAS

AF:

0.721

Gnomad4 FIN

AF:

0.811

Gnomad4 NFE

AF:

0.786

Gnomad4 OTH

AF:

0.783

Alfa

AF:

0.796

Hom.:

8497

Bravo

AF:

0.800

Asia WGS

AF:

0.650

AC:

2263

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

PSAT deficiency

Benign:2

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Oct 25, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jun 14, 2016	- -

Neu-Laxova syndrome 2

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Oct 25, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

1.9

DANN

Benign

0.52

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.2

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over