chr9-78300476-G-A

Position:

• chr9-78300476-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_058179.4(PSAT1):​c.61-126G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 1,209,518 control chromosomes in the GnomAD database, including 18,541 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.14 (1726 hom., cov: 31)
  • Exomes 𝑓: 0.17 (16815 hom.)
• Consequence: PSAT1 NM_058179.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.00200

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BP6: Variant 9-78300476-G-A is Benign according to our data. Variant chr9-78300476-G-A is described in ClinVar as [Benign]. Clinvar id is 1233296.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PSAT1	NM_058179.4	c.61-126G>A		intron_variant		ENST00000376588.4
PSAT1	NM_021154.5	c.61-126G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSAT1	ENST00000376588.4	c.61-126G>A		intron_variant		1	NM_058179.4	P1
PSAT1	ENST00000347159.6	c.61-126G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21152 AN: 152056 Hom.: 1729 Cov.: 31

Gnomad AFR AF: 0.0610

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.155

GnomAD4 exome AF: 0.174 AC: 183695 AN: 1057344 Hom.: 16815 AF XY: 0.173 AC XY: 89635 AN XY: 517864

Gnomad4 AFR exome AF: 0.0538

Gnomad4 AMR exome AF: 0.0958

Gnomad4 ASJ exome AF: 0.203

Gnomad4 EAS exome AF: 0.207

Gnomad4 SAS exome AF: 0.122

Gnomad4 FIN exome AF: 0.114

Gnomad4 NFE exome AF: 0.182

Gnomad4 OTH exome AF: 0.170

GnomAD4 genome AF: 0.139 AC: 21154 AN: 152174 Hom.: 1726 Cov.: 31 AF XY: 0.136 AC XY: 10135 AN XY: 74374

Gnomad4 AFR AF: 0.0610

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.154

Alfa AF: 0.154 Hom.: 260

Bravo AF: 0.137

Asia WGS AF: 0.163 AC: 564 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	5.1
DANN	Benign	0.85
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.3

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: rs3824360; hg19: chr9-80915392; COSMIC: COSV61304076;