1-18871920-G-A

Position:

• chr1-18871920-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_003748.4(ALDH4A1):​c.*925C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,162 control chromosomes in the GnomAD database, including 4,967 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.25 (4962 hom., cov: 34)
  • Exomes 𝑓: 0.24 (5 hom.)
• Consequence: ALDH4A1 NM_003748.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.589

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 1-18871920-G-A is Benign according to our data. Variant chr1-18871920-G-A is described in ClinVar as [Benign]. Clinvar id is 294341.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ALDH4A1	NM_003748.4	c.*925C>T		3_prime_UTR_variant	15/15	ENST00000375341.8
ALDH4A1	NM_001161504.2	c.*925C>T		3_prime_UTR_variant	15/15
ALDH4A1	NM_001319218.2	c.*925C>T		3_prime_UTR_variant	14/14
ALDH4A1	NM_170726.3	c.*42-130C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALDH4A1	ENST00000375341.8	c.*925C>T		3_prime_UTR_variant	15/15	1	NM_003748.4	P1
ALDH4A1	ENST00000538839.5	c.*925C>T		3_prime_UTR_variant	14/14	1
ALDH4A1	ENST00000290597.9	c.*42-130C>T		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38234 AN: 151940 Hom.: 4959 Cov.: 34

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.0346

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.257

GnomAD4 exome AF: 0.240 AC: 25 AN: 104 Hom.: 5 Cov.: 0 AF XY: 0.263 AC XY: 20 AN XY: 76

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.143

Gnomad4 NFE exome AF: 0.263

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.252 AC: 38260 AN: 152058 Hom.: 4962 Cov.: 34 AF XY: 0.245 AC XY: 18230 AN XY: 74312

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.0347

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.259

Alfa AF: 0.253 Hom.: 3357

Bravo AF: 0.255

Asia WGS AF: 0.116 AC: 408 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hyperprolinemia type 2 Benign:1

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. -

not provided Benign:1

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	-0.84
CADD	Benign	5.5
DANN	Benign	0.42

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: rs1140477; hg19: chr1-19198414;