rs7182884

Variant names:

• chr15-100898657-A-C
• rs7182884
• NM_000693.4:c.883+472A>C

Your query was ambiguous. Multiple possible variants found:

• chr15-100898657-A-C
• chr15-100898657-A-T

Variant summary

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

The NM_000693.4(ALDH1A3):​c.883+472A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,152 control chromosomes in the GnomAD database, including 8,506 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 0.31 (8506 hom., cov: 33)
• Consequence: ALDH1A3 NM_000693.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399

Genes affected

ALDH1A3 (HGNC:409): (aldehyde dehydrogenase 1 family member A3) This gene encodes an aldehyde dehydrogenase enzyme that uses retinal as a substrate. Mutations in this gene have been associated with microphthalmia, isolated 8, and expression changes have also been detected in tumor cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]

ALDH1A3-AS1 (HGNC:55416): (ALDH1A3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALDH1A3	NM_000693.4	c.883+472A>C		intron_variant	Intron 8 of 12	ENST00000329841.10	NP_000684.2
ALDH1A3	NM_001293815.2	c.562+472A>C		intron_variant	Intron 5 of 9		NP_001280744.1
ALDH1A3-AS1	NR_135827.1	n.481-2591T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALDH1A3	ENST00000329841.10	c.883+472A>C		intron_variant	Intron 8 of 12	1	NM_000693.4	ENSP00000332256.5

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46745 AN: 152034 Hom.: 8502 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.307 AC: 46754 AN: 152152 Hom.: 8506 Cov.: 33 AF XY: 0.307 AC XY: 22835 AN XY: 74402

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.316

Alfa AF: 0.393 Hom.: 16342

Bravo AF: 0.284

Asia WGS AF: 0.355 AC: 1235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.59
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs7182884; hg19: chr15-101438862; COSMIC: COSV60903141; COSMIC: COSV60903141;