chr15-58032789-AAC-A

Variant names:

• chr15-58032789-AAC-A
• rs59226967
• NM_003888.4:c.118-18510_118-18509delGT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_003888.4(ALDH1A2):​c.118-18510_118-18509delGT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0019 (0 hom., cov: 0)
• Consequence: ALDH1A2 NM_003888.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALDH1A2	NM_003888.4	c.118-18510_118-18509delGT		intron_variant	Intron 1 of 12	ENST00000249750.9	NP_003879.2
ALDH1A2	NM_001206897.2	c.55-18510_55-18509delGT		intron_variant	Intron 2 of 13		NP_001193826.1
ALDH1A2	NM_170696.3	c.118-18510_118-18509delGT		intron_variant	Intron 1 of 11		NP_733797.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALDH1A2	ENST00000249750.9	c.118-18510_118-18509delGT		intron_variant	Intron 1 of 12	1	NM_003888.4	ENSP00000249750.4

Frequencies

GnomAD3 genomes AF: 0.00195 AC: 291 AN: 148932 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00408

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00128

Gnomad ASJ AF: 0.000585

Gnomad EAS AF: 0.000395

Gnomad SAS AF: 0.00191

Gnomad FIN AF: 0.00351

Gnomad MID AF: 0.00323

Gnomad NFE AF: 0.000776

Gnomad OTH AF: 0.00246

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

GnomAD4 genome AF: 0.00195 AC: 290 AN: 149010 Hom.: 0 Cov.: 0 AF XY: 0.00231 AC XY: 168 AN XY: 72600

African (AFR) AF: 0.00405 AC: 165 AN: 40740

American (AMR) AF: 0.00128 AC: 19 AN: 14896

Ashkenazi Jewish (ASJ) AF: 0.000585 AC: 2 AN: 3420

East Asian (EAS) AF: 0.000396 AC: 2 AN: 5048

South Asian (SAS) AF: 0.00191 AC: 9 AN: 4702

European-Finnish (FIN) AF: 0.00351 AC: 35 AN: 9978

Middle Eastern (MID) AF: 0.00347 AC: 1 AN: 288

European-Non Finnish (NFE) AF: 0.000776 AC: 52 AN: 66982

Other (OTH) AF: 0.00244 AC: 5 AN: 2050

Alfa AF: 0.00 Hom.: 623

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.31

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: rs59226967; hg19: chr15-58324987; COSMIC: COSV51077980;