rs2230707

Positions:

• chr1-18876402-G-A

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_003748.4(ALDH4A1):​c.1251C>T​(p.Ala417Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 1,612,090 control chromosomes in the GnomAD database, including 188,387 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.48 (17668 hom., cov: 33)
  • Exomes 𝑓: 0.48 (170719 hom.)
• Consequence: ALDH4A1 NM_003748.4 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:5
• Conservation: PhyloP100: -9.18

Genes affected

ALDH4A1 (HGNC:406): (aldehyde dehydrogenase 4 family member A1) This protein belongs to the aldehyde dehydrogenase family of proteins. This enzyme is a mitochondrial matrix NAD-dependent dehydrogenase which catalyzes the second step of the proline degradation pathway, converting pyrroline-5-carboxylate to glutamate. Deficiency of this enzyme is associated with type II hyperprolinemia, an autosomal recessive disorder characterized by accumulation of delta-1-pyrroline-5-carboxylate (P5C) and proline. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jun 2009]

ACMG classification

Verdict is Benign. Variant got -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BP6: Variant 1-18876402-G-A is Benign according to our data. Variant chr1-18876402-G-A is described in ClinVar as [Benign]. Clinvar id is 294374.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-9.18 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALDH4A1	NM_003748.4	c.1251C>T	p.Ala417Ala	synonymous_variant	12/15	ENST00000375341.8	NP_003739.2
ALDH4A1	NM_170726.3	c.1251C>T	p.Ala417Ala	synonymous_variant	12/16		NP_733844.1
ALDH4A1	NM_001161504.2	c.1071C>T	p.Ala357Ala	synonymous_variant	12/15		NP_001154976.1
ALDH4A1	NM_001319218.2	c.1185+806C>T		intron_variant			NP_001306147.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALDH4A1	ENST00000375341.8	c.1251C>T	p.Ala417Ala	synonymous_variant	12/15	1	NM_003748.4	ENSP00000364490.3
ALDH4A1	ENST00000290597.9	c.1251C>T	p.Ala417Ala	synonymous_variant	12/16	1		ENSP00000290597.5
ALDH4A1	ENST00000538839.5	c.1185+806C>T		intron_variant		1		ENSP00000446071.1
ALDH4A1	ENST00000538309.5	c.1071C>T	p.Ala357Ala	synonymous_variant	12/15	2		ENSP00000442988.1

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72520 AN: 151914 Hom.: 17651 Cov.: 33

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.503

GnomAD3 exomes AF: 0.512 AC: 127294 AN: 248752 Hom.: 33441 AF XY: 0.504 AC XY: 67844 AN XY: 134568

Gnomad AFR exome AF: 0.440

Gnomad AMR exome AF: 0.693

Gnomad ASJ exome AF: 0.500

Gnomad EAS exome AF: 0.608

Gnomad SAS exome AF: 0.499

Gnomad FIN exome AF: 0.435

Gnomad NFE exome AF: 0.470

Gnomad OTH exome AF: 0.515

GnomAD4 exome AF: 0.481 AC: 702251 AN: 1460058 Hom.: 170719 Cov.: 53 AF XY: 0.481 AC XY: 349125 AN XY: 726254

Gnomad4 AFR exome AF: 0.432

Gnomad4 AMR exome AF: 0.687

Gnomad4 ASJ exome AF: 0.497

Gnomad4 EAS exome AF: 0.625

Gnomad4 SAS exome AF: 0.499

Gnomad4 FIN exome AF: 0.436

Gnomad4 NFE exome AF: 0.469

Gnomad4 OTH exome AF: 0.486

GnomAD4 genome AF: 0.477 AC: 72594 AN: 152032 Hom.: 17668 Cov.: 33 AF XY: 0.481 AC XY: 35757 AN XY: 74318

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.505

Alfa AF: 0.484 Hom.: 17568

Bravo AF: 0.492

Asia WGS AF: 0.557 AC: 1940 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hyperprolinemia type 2 Benign:3

Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 14, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 02, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	0.018
DANN	Benign	0.82

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: rs2230707; hg19: chr1-19202896; COSMIC: COSV51891838;