9-78320883-C-T

Variant names:

• chr9-78320883-C-T
• rs11137606
• NM_058179.4:c.869+3079C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_058179.4(PSAT1):​c.869+3079C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,080 control chromosomes in the GnomAD database, including 7,263 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 0.27 (7263 hom., cov: 31)
• Consequence: PSAT1 NM_058179.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.676
• Publications: 2 publications found

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 Gene-Disease associations (from GenCC):

• neurometabolic disorder due to serine deficiency

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• PSAT deficiency

  Inheritance: AD, AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)
• Neu-Laxova syndrome 2

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: G2P, Ambry Genetics
• Neu-Laxova syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSAT1	NM_058179.4	c.869+3079C>T		intron_variant	Intron 7 of 8	ENST00000376588.4	NP_478059.1
PSAT1	NM_021154.5	c.869+3079C>T		intron_variant	Intron 7 of 7		NP_066977.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSAT1	ENST00000376588.4	c.869+3079C>T		intron_variant	Intron 7 of 8	1	NM_058179.4	ENSP00000365773.3
PSAT1	ENST00000347159.6	c.869+3079C>T		intron_variant	Intron 7 of 7	1		ENSP00000317606.2

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40630 AN: 151962 Hom.: 7239 Cov.: 31

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.268 AC: 40713 AN: 152080 Hom.: 7263 Cov.: 31 AF XY: 0.265 AC XY: 19722 AN XY: 74338

African (AFR) AF: 0.505 AC: 20936 AN: 41482

American (AMR) AF: 0.278 AC: 4247 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 646 AN: 3470

East Asian (EAS) AF: 0.298 AC: 1540 AN: 5170

South Asian (SAS) AF: 0.143 AC: 685 AN: 4806

European-Finnish (FIN) AF: 0.127 AC: 1339 AN: 10576

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10521 AN: 67982

Other (OTH) AF: 0.239 AC: 504 AN: 2106

Alfa AF: 0.186 Hom.: 13893

Bravo AF: 0.289

Asia WGS AF: 0.225 AC: 783 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	4.7
DANN	Benign	0.65
PhyloP100		0.68
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11137606; hg19: chr9-80935799;