rs1055637

chr19-49470527-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.69

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]

ACMG classification

Verdict is Benign. Variant got -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	HGVSp	Effect	#exon/exons	MANE	UniProt
ALDH16A1	NM_153329.4	c.*60A>G		3_prime_UTR_variant	17/17	ENST00000293350.9
ALDH16A1	NM_001145396.2	c.*60A>G		3_prime_UTR_variant	16/16
ALDH16A1	XM_011526441.1	c.*60A>G		3_prime_UTR_variant	17/17
ALDH16A1	XM_047438163.1	c.*60A>G		3_prime_UTR_variant	18/18

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALDH16A1	ENST00000293350.9	c.*60A>G		3_prime_UTR_variant	17/17	1	NM_153329.4	P1

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62589 AN: 151856 Hom.: 13908 Cov.: 31

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.: 28 AF XY: 0.345 AC XY: 214961 AN XY: 622298

Gnomad4 AFR exome AF: 0.601

Gnomad4 AMR exome AF: 0.260

Gnomad4 ASJ exome AF: 0.443

Gnomad4 EAS exome AF: 0.249

Gnomad4 SAS exome AF: 0.399

Gnomad4 FIN exome AF: 0.356

Gnomad4 NFE exome AF: 0.334

Gnomad4 OTH exome AF: 0.360

GnomAD4 genome AF: 0.412 AC: 62653 AN: 151974 Hom.: 13922 Cov.: 31 AF XY: 0.411 AC XY: 30533 AN XY: 74266

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.409

Alfa AF: 0.366 Hom.: 10264

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
Dann	Benign	0.66

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: rs1055637; hg19: chr19-49973784; COSMIC: COSV52619085; COSMIC: COSV52619085;