15-58398555-G-A

Position:

• chr15-58398555-G-A

Variant summary

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

The ENST00000558239.5(ALDH1A2):​c.-172+21416C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,100 control chromosomes in the GnomAD database, including 12,282 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 0.38 (12282 hom., cov: 32)
• Consequence: ALDH1A2 ENST00000558239.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221

Genes affected

ALDH1A2 (HGNC:15472): (aldehyde dehydrogenase 1 family member A2) This protein belongs to the aldehyde dehydrogenase family of proteins. The product of this gene is an enzyme that catalyzes the synthesis of retinoic acid (RA) from retinaldehyde. Retinoic acid, the active derivative of vitamin A (retinol), is a hormonal signaling molecule that functions in developing and adult tissues. The studies of a similar mouse gene suggest that this enzyme and the cytochrome CYP26A1, concurrently establish local embryonic retinoic acid levels which facilitate posterior organ development and prevent spina bifida. Four transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, May 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALDH1A2	ENST00000558239.5	c.-172+21416C>T		intron_variant		4		ENSP00000453292
ALDH1A2	ENST00000560863.5	n.415+21416C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.375 AC: 57050 AN: 151982 Hom.: 12279 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.396

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.375 AC: 57079 AN: 152100 Hom.: 12282 Cov.: 32 AF XY: 0.373 AC XY: 27746 AN XY: 74346

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.394

Alfa AF: 0.456 Hom.: 33107

Bravo AF: 0.374

Asia WGS AF: 0.240 AC: 836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.72

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs415799; hg19: chr15-58690754;