chr9-78297481-C-G

Position:

• chr9-78297481-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_058179.4(PSAT1):​c.60+211C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 152,174 control chromosomes in the GnomAD database, including 44,344 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.76 (44344 hom., cov: 34)
• Consequence: PSAT1 NM_058179.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.37

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 9-78297481-C-G is Benign according to our data. Variant chr9-78297481-C-G is described in ClinVar as [Benign]. Clinvar id is 1296838.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PSAT1	NM_058179.4	c.60+211C>G		intron_variant		ENST00000376588.4	NP_478059.1
PSAT1	NM_021154.5	c.60+211C>G		intron_variant			NP_066977.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PSAT1	ENST00000376588.4	c.60+211C>G		intron_variant		1	NM_058179.4	ENSP00000365773	P1
PSAT1	ENST00000347159.6	c.60+211C>G		intron_variant		1		ENSP00000317606

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115832 AN: 152056 Hom.: 44316 Cov.: 34

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.762 AC: 115912 AN: 152174 Hom.: 44344 Cov.: 34 AF XY: 0.761 AC XY: 56632 AN XY: 74390

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.818

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.670

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.772

Gnomad4 OTH AF: 0.767

Alfa AF: 0.779 Hom.: 5737

Bravo AF: 0.767

Asia WGS AF: 0.639 AC: 2224 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	-0.90
CADD	Benign	1.3
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs10746571; hg19: chr9-80912397;