Variant chr6-134932896-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_022568.4(ALDH8A1):c.729C>T(p.Ser243=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00162 in 1,614,198 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0084 ( 19 hom., cov: 32)

Exomes 𝑓: 0.00092 ( 18 hom. )

Consequence

ALDH8A1
NM_022568.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0560

Variant links:

Genes affected

ALDH8A1 (HGNC:15471): (aldehyde dehydrogenase 8 family member A1) This gene encodes a member of the aldehyde dehydrogenase family of proteins. The encoded protein has been implicated in the synthesis of 9-cis-retinoic acid and in the breakdown of the amino acid tryptophan. This enzyme converts 9-cis-retinal into the retinoid X receptor ligand 9-cis-retinoic acid, and has approximately 40-fold higher activity with 9-cis-retinal than with all-trans-retinal. In addition, this enzyme has been shown to catalyze the conversion of 2-aminomuconic semialdehyde to 2-aminomuconate in the kynurenine pathway of tryptophan catabolism. [provided by RefSeq, Jul 2018]

ALDH8A1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 6-134932896-G-A is Benign according to our data. Variant chr6-134932896-G-A is described in ClinVar as [Benign]. Clinvar id is 716950.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.056 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00838 (1277/152344) while in subpopulation AFR AF= 0.0289 (1200/41580). AF 95% confidence interval is 0.0275. There are 19 homozygotes in gnomad4. There are 592 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 19 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
ALDH8A1	NM_022568.4 linkuse as main transcript	c.729C>T	p.Ser243=	synonymous_variant	5/7	ENST00000265605.7
ALDH8A1	NM_001193480.2 linkuse as main transcript	c.579C>T	p.Ser193=	synonymous_variant	4/6
ALDH8A1	NM_170771.3 linkuse as main transcript	c.729C>T	p.Ser243=	synonymous_variant	5/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALDH8A1	ENST00000265605.7 linkuse as main transcript	c.729C>T	p.Ser243=	synonymous_variant	5/7	1	NM_022568.4	P1	Q9H2A2-1
ALDH8A1	ENST00000367845.6 linkuse as main transcript	c.729C>T	p.Ser243=	synonymous_variant	5/6	1			Q9H2A2-2
ALDH8A1	ENST00000349305.8 linkuse as main transcript	c.*287C>T		3_prime_UTR_variant, NMD_transcript_variant	6/7	1			Q9H2A2-3
ALDH8A1	ENST00000367847.2 linkuse as main transcript	c.579C>T	p.Ser193=	synonymous_variant	4/6	2			Q9H2A2-4

Frequencies

GnomAD3 genomes

AF:

0.00838

AC:

1276

AN:

152226

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0289

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00294

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.000282

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.000147

Gnomad OTH

AF:

0.00670

GnomAD3 exomes

AF:

0.00228

AC:

573

AN:

251258

Hom.:

AF XY:

0.00161

AC XY:

219

AN XY:

135790

show subpopulations

Gnomad AFR exome

AF:

0.0300

Gnomad AMR exome

AF:

0.00176

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000653

Gnomad FIN exome

AF:

0.000139

Gnomad NFE exome

AF:

0.0000792

Gnomad OTH exome

AF:

0.00163

GnomAD4 exome

AF:

0.000919

AC:

1344

AN:

1461854

Hom.:

Cov.:

AF XY:

0.000785

AC XY:

571

AN XY:

727228

show subpopulations

Gnomad4 AFR exome

AF:

0.0302

Gnomad4 AMR exome

AF:

0.00186

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0000696

Gnomad4 FIN exome

AF:

0.000206

Gnomad4 NFE exome

AF:

0.0000620

Gnomad4 OTH exome

AF:

0.00250

GnomAD4 genome

AF:

0.00838

AC:

1277

AN:

152344

Hom.:

Cov.:

AF XY:

0.00795

AC XY:

592

AN XY:

74484

show subpopulations

Gnomad4 AFR

AF:

0.0289

Gnomad4 AMR

AF:

0.00294

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000414

Gnomad4 FIN

AF:

0.000282

Gnomad4 NFE

AF:

0.000147

Gnomad4 OTH

AF:

0.00664

Alfa

AF:

0.00404

Hom.:

Bravo

AF:

0.00954

Asia WGS

AF:

0.00346

AC:

AN:

3478

EpiCase

AF:

0.000164

EpiControl

AF:

0.000119

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

May 15, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

1.2

DANN

Benign

0.46

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