rs2230705

chr1-18877503-C-Gchr1-18877503-C-T

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_Moderate BP6_Very_Strong BP7 BA1

The NM_003748.4(ALDH4A1):c.1050G>C(p.Ala350=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 1,607,222 control chromosomes in the GnomAD database, including 408,905 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.71 (38646 hom., cov: 33)
  • Exomes 𝑓: 0.71 (370259 hom.)
• Consequence: ALDH4A1 NM_003748.4 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 1.60

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 -19 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BP6: Variant 1-18877503-C-G is Benign according to our data. Variant chr1-18877503-C-G is described in ClinVar as [Benign]. Clinvar id is 294382.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-18877503-C-G is described in Lovd as [Benign].
• BP7: Synonymous conserved (PhyloP=1.6 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALDH4A1	NM_003748.4	c.1050G>C	p.Ala350=	synonymous_variant	10/15	ENST00000375341.8
ALDH4A1	NM_170726.3	c.1050G>C	p.Ala350=	synonymous_variant	10/16
ALDH4A1	NM_001319218.2	c.1050G>C	p.Ala350=	synonymous_variant	10/14
ALDH4A1	NM_001161504.2	c.870G>C	p.Ala290=	synonymous_variant	10/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALDH4A1	ENST00000375341.8	c.1050G>C	p.Ala350=	synonymous_variant	10/15	1	NM_003748.4	P1
ALDH4A1	ENST00000290597.9	c.1050G>C	p.Ala350=	synonymous_variant	10/16	1		P1
ALDH4A1	ENST00000538839.5	c.1050G>C	p.Ala350=	synonymous_variant	10/14	1
ALDH4A1	ENST00000538309.5	c.870G>C	p.Ala290=	synonymous_variant	10/15	2

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107923 AN: 152036 Hom.: 38609 Cov.: 33

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.696

GnomAD3 exomes AF: 0.689 AC: 164889 AN: 239156 Hom.: 57758 AF XY: 0.683 AC XY: 88592 AN XY: 129734

Gnomad AFR exome AF: 0.723

Gnomad AMR exome AF: 0.746

Gnomad ASJ exome AF: 0.619

Gnomad EAS exome AF: 0.449

Gnomad SAS exome AF: 0.590

Gnomad FIN exome AF: 0.801

Gnomad NFE exome AF: 0.719

Gnomad OTH exome AF: 0.700

GnomAD4 exome AF: 0.710 AC: 1033651 AN: 1455068 Hom.: 370259 Cov.: 76 AF XY: 0.706 AC XY: 510376 AN XY: 723282

Gnomad4 AFR exome AF: 0.724

Gnomad4 AMR exome AF: 0.744

Gnomad4 ASJ exome AF: 0.624

Gnomad4 EAS exome AF: 0.456

Gnomad4 SAS exome AF: 0.588

Gnomad4 FIN exome AF: 0.799

Gnomad4 NFE exome AF: 0.727

Gnomad4 OTH exome AF: 0.688

GnomAD4 genome AF: 0.710 AC: 108017 AN: 152154 Hom.: 38646 Cov.: 33 AF XY: 0.711 AC XY: 52891 AN XY: 74388

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.582

Gnomad4 FIN AF: 0.807

Gnomad4 NFE AF: 0.719

Gnomad4 OTH AF: 0.691

Alfa AF: 0.693 Hom.: 9493

Bravo AF: 0.705

Asia WGS AF: 0.520 AC: 1813 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hyperprolinemia type 2 Benign:3

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 14, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 12, 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	Invitae	Feb 01, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
Cadd	Benign	8.7
Dann	Benign	0.74

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: rs2230705; hg19: chr1-19203997; COSMIC: COSV51892136;