dbSNP rs1055637: ALDH16A1:c.*60A>G (chr19-49470527-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_153329.4(ALDH16A1):c.*60A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 1,433,308 control chromosomes in the GnomAD database, including 91,791 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.41 ( 13922 hom., cov: 31)

Exomes 𝑓: 0.34 ( 77869 hom. )

Consequence

ALDH16A1
NM_153329.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.69

Publications

19 publications found

Variant links:

Genes affected

ALDH16A1 (HGNC:28114): (aldehyde dehydrogenase 16 family member A1) This gene encodes a member of the aldehyde dehydrogenase superfamily. The family members act on aldehyde substrates and use nicotinamide adenine dinucleotide phosphate (NADP) as a cofactor. This gene is conserved in chimpanzee, dog, cow, mouse, rat, and zebrafish. The protein encoded by this gene interacts with maspardin, a protein that when truncated is responsible for Mast syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2010]

ALDH16A1 links:

ENSG00000269469 (HGNC:):

ENSG00000269469 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ALDH16A1	NM_153329.4 link	c.*60A>G	3_prime_UTR_variant	Exon 17 of 17	ENST00000293350.9	NP_699160.2	Q8IZ83-1
ALDH16A1	NM_001145396.2 link	c.*60A>G	3_prime_UTR_variant	Exon 16 of 16		NP_001138868.1	Q8IZ83-3
ALDH16A1	XM_011526441.1 link	c.*60A>G	3_prime_UTR_variant	Exon 17 of 17		XP_011524743.1
ALDH16A1	XM_047438163.1 link	c.*60A>G	3_prime_UTR_variant	Exon 18 of 18		XP_047294119.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALDH16A1	ENST00000293350.9 link	c.*60A>G		3_prime_UTR_variant	Exon 17 of 17	1	NM_153329.4	ENSP00000293350.3		Q8IZ83-1
ENSG00000269469	ENST00000599536.1 link	n.*121-4076A>G		intron_variant	Intron 4 of 5	5		ENSP00000470318.1		M0QZ58

Frequencies

GnomAD3 genomes

AF:

0.412

AC:

62589

AN:

151856

Hom.:

13908

Cov.:

show subpopulations

Gnomad AFR

AF:

0.581

Gnomad AMI

AF:

0.240

Gnomad AMR

AF:

0.317

Gnomad ASJ

AF:

0.458

Gnomad EAS

AF:

0.289

Gnomad SAS

AF:

0.387

Gnomad FIN

AF:

0.367

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.349

Gnomad OTH

AF:

0.407

GnomAD4 exome

AF:

0.344

AC:

440249

AN:

1281334

Hom.:

77869

Cov.:

AF XY:

0.345

AC XY:

214961

AN XY:

622298

show subpopulations

African (AFR)

AF:

0.601

AC:

16055

AN:

26700

American (AMR)

AF:

0.260

AC:

4807

AN:

18508

Ashkenazi Jewish (ASJ)

AF:

0.443

AC:

8140

AN:

18382

East Asian (EAS)

AF:

0.249

AC:

7934

AN:

31868

South Asian (SAS)

AF:

0.399

AC:

25207

AN:

63156

European-Finnish (FIN)

AF:

0.356

AC:

15400

AN:

43310

Middle Eastern (MID)

AF:

0.512

AC:

1807

AN:

3532

European-Non Finnish (NFE)

AF:

0.334

AC:

341942

AN:

1023210

Other (OTH)

AF:

0.360

AC:

18957

AN:

52668

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

14809

29618

44427

59236

74045

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.412

AC:

62653

AN:

151974

Hom.:

13922

Cov.:

AF XY:

0.411

AC XY:

30533

AN XY:

74266

show subpopulations

African (AFR)

AF:

0.581

AC:

24078

AN:

41442

American (AMR)

AF:

0.317

AC:

4829

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.458

AC:

1589

AN:

3472

East Asian (EAS)

AF:

0.289

AC:

1491

AN:

5158

South Asian (SAS)

AF:

0.389

AC:

1873

AN:

4818

European-Finnish (FIN)

AF:

0.367

AC:

3883

AN:

10572

Middle Eastern (MID)

AF:

0.483

AC:

141

AN:

292

European-Non Finnish (NFE)

AF:

0.349

AC:

23688

AN:

67950

Other (OTH)

AF:

0.409

AC:

862

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1747

3494

5240

6987

8734

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.372

Hom.:

15800

Bravo

AF:

0.412

Asia WGS

AF:

0.357

AC:

1242

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.17

(source)

DANN

Benign

0.66

PhyloP100

-4.7

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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rs1055637

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over