rs41277897

Variant names:

• chr9-78304891-G-A
• rs41277897
• NM_058179.4:c.348G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-78304891-G-A
• chr9-78304891-G-C
• chr9-78304891-G-T

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_Strong BS1 BS2

The NM_058179.4(PSAT1):​c.348G>A​(p.Lys116Lys) variant causes a synonymous change. The variant allele was found at a frequency of 0.00996 in 1,613,654 control chromosomes in the GnomAD database, including 183 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0092 (20 hom., cov: 33)
  • Exomes 𝑓: 0.010 (163 hom.)
• Consequence: PSAT1 NM_058179.4 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 5.45

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

Our verdict: Benign. The variant received -16 ACMG points.

• BP6: Variant 9-78304891-G-A is Benign according to our data. Variant chr9-78304891-G-A is described in ClinVar as [Benign]. Clinvar id is 542040.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.00922 (1404/152324) while in subpopulation NFE AF = 0.0146 (994/68030). AF 95% confidence interval is 0.0139. There are 20 homozygotes in GnomAd4. There are 692 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position FAILED quality control check.
• BS2: High Homozygotes in GnomAd4 at 20 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSAT1	NM_058179.4	c.348G>A	p.Lys116Lys	synonymous_variant	Exon 4 of 9	ENST00000376588.4	NP_478059.1
PSAT1	NM_021154.5	c.348G>A	p.Lys116Lys	synonymous_variant	Exon 4 of 8		NP_066977.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PSAT1	ENST00000376588.4	c.348G>A	p.Lys116Lys	synonymous_variant	Exon 4 of 9	1	NM_058179.4	ENSP00000365773.3
PSAT1	ENST00000347159.6	c.348G>A	p.Lys116Lys	synonymous_variant	Exon 4 of 8	1		ENSP00000317606.2

Frequencies

GnomAD3 genomes AF: 0.00921 AC: 1402 AN: 152206 Hom.: 20 Cov.: 33

Gnomad AFR AF: 0.00133

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.00347

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00289

Gnomad FIN AF: 0.0210

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0146

Gnomad OTH AF: 0.00621

GnomAD2 exomes AF: 0.00911 AC: 2292 AN: 251476 AF XY: 0.00900

Gnomad AFR exome AF: 0.00105

Gnomad AMR exome AF: 0.00208

Gnomad ASJ exome AF: 0.00764

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0183

Gnomad NFE exome AF: 0.0141

Gnomad OTH exome AF: 0.00766

GnomAD4 exome AF: 0.0100 AC: 14667 AN: 1461330 Hom.: 163 Cov.: 36 AF XY: 0.0101 AC XY: 7346 AN XY: 726986

Gnomad4 AFR exome AF: 0.00123 AC: 41 AN: 33468

Gnomad4 AMR exome AF: 0.00197 AC: 88 AN: 44724

Gnomad4 ASJ exome AF: 0.00627 AC: 164 AN: 26136

Gnomad4 EAS exome AF: 0.0000252 AC: 1 AN: 39700

Gnomad4 SAS exome AF: 0.00255 AC: 220 AN: 86228

Gnomad4 FIN exome AF: 0.0201 AC: 1074 AN: 53420

Gnomad4 NFE exome AF: 0.0113 AC: 12594 AN: 1111980

Gnomad4 Remaining exome AF: 0.00799 AC: 482 AN: 60338

GnomAD4 genome AF: 0.00922 AC: 1404 AN: 152324 Hom.: 20 Cov.: 33 AF XY: 0.00929 AC XY: 692 AN XY: 74476

Gnomad4 AFR AF: 0.00132 AC: 0.00132288 AN: 0.00132288

Gnomad4 AMR AF: 0.00346 AC: 0.00346315 AN: 0.00346315

Gnomad4 ASJ AF: 0.00749 AC: 0.0074928 AN: 0.0074928

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.00331 AC: 0.00331126 AN: 0.00331126

Gnomad4 FIN AF: 0.0210 AC: 0.02101 AN: 0.02101

Gnomad4 NFE AF: 0.0146 AC: 0.0146112 AN: 0.0146112

Gnomad4 OTH AF: 0.00615 AC: 0.00614948 AN: 0.00614948

Alfa AF: 0.0131 Hom.: 16

Bravo AF: 0.00706

Asia WGS AF: 0.00144 AC: 5 AN: 3478

EpiCase AF: 0.0133

EpiControl AF: 0.00806

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

May 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PSAT1: BS1, BS2 -

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Neu-Laxova syndrome 2 Benign:1

Feb 02, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	9.1
DANN	Benign	0.69
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.32		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.32		Position offset: 49

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs41277897; hg19: chr9-80919807; COSMIC: COSV100716534;