9-78325660-G-A

Position:

• chr9-78325660-G-A

Variant summary

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

The NM_058179.4(PSAT1):​c.870-2391G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0751 in 152,176 control chromosomes in the GnomAD database, including 529 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 0.075 (529 hom., cov: 33)
• Consequence: PSAT1 NM_058179.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

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]

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 (SAS) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSAT1	NM_058179.4	c.870-2391G>A		intron_variant		ENST00000376588.4	NP_478059.1
PSAT1	NM_021154.5	c.870-3321G>A		intron_variant			NP_066977.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSAT1	ENST00000376588.4	c.870-2391G>A		intron_variant		1	NM_058179.4	ENSP00000365773.3
PSAT1	ENST00000347159.6	c.870-3321G>A		intron_variant		1		ENSP00000317606.2

Frequencies

GnomAD3 genomes AF: 0.0751 AC: 11422 AN: 152058 Hom.: 529 Cov.: 33

Gnomad AFR AF: 0.0230

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0623

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0448

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0751 AC: 11436 AN: 152176 Hom.: 529 Cov.: 33 AF XY: 0.0753 AC XY: 5599 AN XY: 74400

Gnomad4 AFR AF: 0.0231

Gnomad4 AMR AF: 0.0624

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.0451

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.0672

Alfa AF: 0.0887 Hom.: 535

Bravo AF: 0.0671

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.59

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: rs1411916; hg19: chr9-80940576;