Variant 1-18872082-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

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

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -4.53

Variant links:

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]

ALDH4A1 links:

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ACMG classification

Classification made for transcript

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	Effect	#exon/exons	MANE
ALDH4A1	NM_003748.4 linkuse as main transcript	c.*763T>C	3_prime_UTR_variant	15/15	ENST00000375341.8
ALDH4A1	NM_001161504.2 linkuse as main transcript	c.*763T>C	3_prime_UTR_variant	15/15
ALDH4A1	NM_001319218.2 linkuse as main transcript	c.*763T>C	3_prime_UTR_variant	14/14
ALDH4A1	NM_170726.3 linkuse as main transcript	c.*42-292T>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALDH4A1	ENST00000375341.8 linkuse as main transcript	c.*763T>C	3_prime_UTR_variant	15/15	1	NM_003748.4	P1	P30038-1
ALDH4A1	ENST00000538839.5 linkuse as main transcript	c.*763T>C	3_prime_UTR_variant	14/14	1			P30038-3
ALDH4A1	ENST00000290597.9 linkuse as main transcript	c.*42-292T>C	intron_variant		1		P1	P30038-1

Frequencies

GnomAD3 genomes

AF:

0.659

AC:

100164

AN:

152038

Hom.:

33624

Cov.:

show subpopulations

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:

AN:

122

Hom.:

Cov.:

AF XY:

0.713

AC XY:

AN XY:

show subpopulations

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.:

AF XY:

0.662

AC XY:

49226

AN XY:

74396

show subpopulations

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

LINK: link

Submissions by phenotype

Hyperprolinemia type 2

Benign:1

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. -

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

-0.90

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over