chr1-18872082-A-G

Variant names:

• chr1-18872082-A-G
• rs1138267
• NM_003748.4:c.*763T>C

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.*763T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 152,280 control chromosomes in the GnomAD database, including 33,684 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.66 (33654 hom., cov: 34)
  • Exomes 𝑓: 0.70 (30 hom.)
• Consequence: ALDH4A1 NM_003748.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -4.53

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=-0.9).
• BP6: Variant 1-18872082-A-G is Benign according to our data. Variant chr1-18872082-A-G is described in ClinVar as [Benign]. Clinvar id is 294344.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALDH4A1	NM_003748.4	c.*763T>C		3_prime_UTR_variant	Exon 15 of 15	ENST00000375341.8	NP_003739.2
ALDH4A1	NM_001319218.2	c.*763T>C		3_prime_UTR_variant	Exon 14 of 14		NP_001306147.1
ALDH4A1	NM_001161504.2	c.*763T>C		3_prime_UTR_variant	Exon 15 of 15		NP_001154976.1
ALDH4A1	NM_170726.3	c.*42-292T>C		intron_variant	Intron 15 of 15		NP_733844.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALDH4A1	ENST00000375341	c.*763T>C		3_prime_UTR_variant	Exon 15 of 15	1	NM_003748.4	ENSP00000364490.3
ALDH4A1	ENST00000538839	c.*763T>C		3_prime_UTR_variant	Exon 14 of 14	1		ENSP00000446071.1
ALDH4A1	ENST00000290597.9	c.*42-292T>C		intron_variant	Intron 15 of 15	1		ENSP00000290597.5

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100164 AN: 152038 Hom.: 33624 Cov.: 34

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.707

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.687

GnomAD4 exome AF: 0.697 AC: 85 AN: 122 Hom.: 30 Cov.: 0 AF XY: 0.713 AC XY: 67 AN XY: 94

Gnomad4 AFR exome AF: 0.750

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.686

Gnomad4 OTH exome AF: 0.833

GnomAD4 genome AF: 0.659 AC: 100242 AN: 152158 Hom.: 33654 Cov.: 34 AF XY: 0.662 AC XY: 49226 AN XY: 74396

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.715

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.688

Alfa AF: 0.696 Hom.: 37421

Bravo AF: 0.661

Asia WGS AF: 0.716 AC: 2493 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:1

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Hyperprolinemia type 2 Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.027
DANN	Benign	0.35
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs1138267; hg19: chr1-19198576;