rs1055637

Variant names:

• chr19-49470527-A-G
• rs1055637
• NM_153329.4:c.*60A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 publications found

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]

ENSG00000269469 (HGNC:):

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153329.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALDH16A1	NM_153329.4	MANE Select	c.*60A>G		3_prime_UTR	Exon 17 of 17	NP_699160.2
	ALDH16A1	NM_001145396.2		c.*60A>G		3_prime_UTR	Exon 16 of 16	NP_001138868.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ALDH16A1	ENST00000293350.9	TSL:1 MANE Select	c.*60A>G		3_prime_UTR	Exon 17 of 17	ENSP00000293350.3
	ENSG00000269469	ENST00000599536.1	TSL:5	n.*121-4076A>G		intron	N/A	ENSP00000470318.1
	ALDH16A1	ENST00000593417.5	TSL:2	n.*1927A>G		non_coding_transcript_exon	Exon 15 of 15	ENSP00000470160.1

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

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

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

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.17
DANN	Benign	0.66
PhyloP100		-4.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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