9-130452225-C-T

Variant names:

• chr9-130452225-C-T
• rs138350285
• NM_054012.4:c.-4C>T

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_Strong BS1_Supporting BS2

The NM_054012.4(ASS1):​c.-4C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000307 in 1,614,052 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.00037 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00030 (3 hom.)
• Consequence: ASS1 NM_054012.4 5_prime_UTR_premature_start_codon_gain
• Scores: Splicing: ADA: 0.0004396
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:7 B:1
• Conservation: PhyloP100: 0.221

Genes affected

ASS1 (HGNC:758): (argininosuccinate synthase 1) The protein encoded by this gene catalyzes the penultimate step of the arginine biosynthetic pathway. There are approximately 10 to 14 copies of this gene including the pseudogenes scattered across the human genome, among which the one located on chromosome 9 appears to be the only functional gene for argininosuccinate synthetase. Mutations in the chromosome 9 copy of this gene cause citrullinemia. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Aug 2012]

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BS1: Variant frequency is greater than expected in population mid. GnomAdExome4 allele frequency = 0.0003 (438/1461734) while in subpopulation MID AF = 0.00624 (36/5768). AF 95% confidence interval is 0.00463. There are 3 homozygotes in GnomAdExome4. There are 292 alleles in the male GnomAdExome4 subpopulation. Median coverage is 32. This position FAILED quality control check. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
• BS2: High Homozygotes in GnomAdExome4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ASS1	NM_054012.4	c.-4C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 2 of 15	ENST00000352480.10	NP_446464.1
ASS1	NM_054012.4	c.-4C>T		splice_region_variant	Exon 2 of 15	ENST00000352480.10	NP_446464.1
ASS1	NM_054012.4	c.-4C>T		5_prime_UTR_variant	Exon 2 of 15	ENST00000352480.10	NP_446464.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ASS1	ENST00000352480	c.-4C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 2 of 15	1	NM_054012.4	ENSP00000253004.6
ASS1	ENST00000352480.10	c.-4C>T		splice_region_variant	Exon 2 of 15	1	NM_054012.4	ENSP00000253004.6
ASS1	ENST00000352480	c.-4C>T		5_prime_UTR_variant	Exon 2 of 15	1	NM_054012.4	ENSP00000253004.6

Frequencies

GnomAD3 genomes AF: 0.000381 AC: 58 AN: 152200 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000531

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000458

Gnomad ASJ AF: 0.000864

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00125

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.000206

Gnomad OTH AF: 0.000478

GnomAD2 exomes AF: 0.000558 AC: 140 AN: 250834 AF XY: 0.000685

Gnomad AFR exome AF: 0.000617

Gnomad AMR exome AF: 0.000695

Gnomad ASJ exome AF: 0.000497

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000309

Gnomad OTH exome AF: 0.00180

GnomAD4 exome AF: 0.000300 AC: 438 AN: 1461734 Hom.: 3 Cov.: 32 AF XY: 0.000402 AC XY: 292 AN XY: 727166

Gnomad4 AFR exome AF: 0.000807 AC: 27 AN: 33478

Gnomad4 AMR exome AF: 0.000626 AC: 28 AN: 44718

Gnomad4 ASJ exome AF: 0.000574 AC: 15 AN: 26132

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

Gnomad4 SAS exome AF: 0.00179 AC: 154 AN: 86226

Gnomad4 FIN exome AF: 0.0000187 AC: 1 AN: 53392

Gnomad4 NFE exome AF: 0.000137 AC: 152 AN: 1111926

Gnomad4 Remaining exome AF: 0.000397 AC: 24 AN: 60394

GnomAD4 genome AF: 0.000374 AC: 57 AN: 152318 Hom.: 0 Cov.: 32 AF XY: 0.000309 AC XY: 23 AN XY: 74484

Gnomad4 AFR AF: 0.000529 AC: 0.000528999 AN: 0.000528999

Gnomad4 AMR AF: 0.000458 AC: 0.000457516 AN: 0.000457516

Gnomad4 ASJ AF: 0.000864 AC: 0.000864055 AN: 0.000864055

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.00125 AC: 0.00124636 AN: 0.00124636

Gnomad4 FIN AF: 0.00 AC: 0 AN: 0

Gnomad4 NFE AF: 0.000206 AC: 0.000205792 AN: 0.000205792

Gnomad4 OTH AF: 0.000473 AC: 0.000473485 AN: 0.000473485

Alfa AF: 0.000237 Hom.: 3

Bravo AF: 0.000476

Asia WGS AF: 0.000577 AC: 2 AN: 3478

EpiCase AF: 0.000436

EpiControl AF: 0.000474

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:7 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Citrullinemia type I Uncertain:5

May 18, 2021

Genome-Nilou Lab

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 11, 2023

Molecular Genetics, Royal Melbourne Hospital

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change in ASS1 is located in the 5' untranslated region. It introduces an alternative initiation codon and alters the Kozak consensus sequence, which plays an essential role in protein translation initiation. No functional assays have been reported to assess if the variant affects protein translation. The highest population minor allele frequency in the population database gnomAD v2.1 is 0.18% (55/30,574 alleles) in the South Asian population. This variant has been reported as likely pathogenic, a variant of uncertain significance, and likely benign (ClinVar ID: 203632). This variant has been observed with a variant of uncertain significance in an individual with citrullinaemia (PMID: 28111830). Based on the classification scheme RMH Modified ACMG Guidelines v1.6.1, this variant is classified as a VARIANT OF UNCERTAIN SIGNIFICANCE. Following criteria are met: none. -

Oct 01, 2021

Myriad Genetics, Inc.

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

NM_000050.4(ASS1):c.-4C>T is a 5' non-coding variant classified as a variant of uncertain significance in the context of citrullinemia type 1. c.-4C>T has been observed in a case with relevant disease (PMID: 28111830). Functional assessments of this variant are not available in the literature. c.-4C>T has been observed in population frequency databases (gnomAD: SAS 0.18%). In summary, there is insufficient evidence to classify NM_000050.4(ASS1):c.-4C>T as pathogenic or benign. Please note: this variant was assessed in the context of healthy population screening. -

Apr 27, 2017

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -

Jun 21, 2021

Natera, Inc.

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided Pathogenic:1 Uncertain:1

Oct 23, 2020

Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 29, 2019

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Previously reported in association with citrullinemia type I (Engel et al., 2009); Nucleotide substitution has no predicted effect on splicing and is not conserved across species; Alters the Kozak consensus sequence, which plays an important role in the initiation of protein translation; This variant is associated with the following publications: (PMID: 25087612, 19006241) -

not specified Uncertain:1

Apr 13, 2023

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: ASS1 c.-4C>T is located in the untranslated mRNA region upstream of the initiation codon. The variant allele was found at a frequency of 0.00056 in 250834 control chromosomes in the gnomAD database, including 1 homozygotes. This frequency is not significantly higher than estimated for a pathogenic variant in ASS1 causing Citrullinemia Type I (0.00056 vs 0.0041), allowing no conclusion about variant significance. The variant was reported in the literature without strong evidence for causality. To our knowledge, no experimental evidence demonstrating its impact on protein function have been reported. Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified as VUS (n=5), Likely Pathogenic (n=1) and Likely Benign (n=1). Based on the evidence outlined above, the variant was classified as uncertain significance. -

Citrullinemia Benign:1

Sep 08, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely 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	-0.75
CADD	Benign	7.2
DANN	Benign	0.70
Mutation Taster		=300/0	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00044
dbscSNV1_RF	Benign	0.040
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: rs138350285; hg19: chr9-133327612;