Variant chr15-100885414-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000693.4(ALDH1A3):c.204+43G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0243 in 1,410,246 control chromosomes in the GnomAD database, including 605 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.030 ( 119 hom., cov: 32)

Exomes 𝑓: 0.024 ( 486 hom. )

Consequence

ALDH1A3
NM_000693.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.566

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 15-100885414-G-T is Benign according to our data. Variant chr15-100885414-G-T is described in ClinVar as [Benign]. Clinvar id is 1286007.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALDH1A3	NM_000693.4 linkuse as main transcript	c.204+43G>T		intron_variant		ENST00000329841.10	NP_000684.2
ALDH1A3	NM_001293815.2 linkuse as main transcript	c.204+43G>T		intron_variant			NP_001280744.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALDH1A3	ENST00000329841.10 linkuse as main transcript	c.204+43G>T		intron_variant		1	NM_000693.4	ENSP00000332256	P1

Frequencies

GnomAD3 genomes

AF:

0.0294

AC:

4481

AN:

152168

Hom.:

114

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0518

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0197

Gnomad ASJ

AF:

0.0576

Gnomad EAS

AF:

0.0348

Gnomad SAS

AF:

0.0474

Gnomad FIN

AF:

0.00349

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0193

Gnomad OTH

AF:

0.0320

GnomAD3 exomes

AF:

0.0250

AC:

6030

AN:

241682

Hom.:

106

AF XY:

0.0253

AC XY:

3324

AN XY:

131160

show subpopulations

Gnomad AFR exome

AF:

0.0546

Gnomad AMR exome

AF:

0.0130

Gnomad ASJ exome

AF:

0.0596

Gnomad EAS exome

AF:

0.0302

Gnomad SAS exome

AF:

0.0428

Gnomad FIN exome

AF:

0.00369

Gnomad NFE exome

AF:

0.0196

Gnomad OTH exome

AF:

0.0228

GnomAD4 exome

AF:

0.0237

AC:

29808

AN:

1257960

Hom.:

486

Cov.:

AF XY:

0.0243

AC XY:

15486

AN XY:

636208

show subpopulations

Gnomad4 AFR exome

AF:

0.0544

Gnomad4 AMR exome

AF:

0.0135

Gnomad4 ASJ exome

AF:

0.0559

Gnomad4 EAS exome

AF:

0.0419

Gnomad4 SAS exome

AF:

0.0433

Gnomad4 FIN exome

AF:

0.00439

Gnomad4 NFE exome

AF:

0.0206

Gnomad4 OTH exome

AF:

0.0275

GnomAD4 genome

AF:

0.0296

AC:

4503

AN:

152286

Hom.:

119

Cov.:

AF XY:

0.0289

AC XY:

2154

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.0522

Gnomad4 AMR

AF:

0.0196

Gnomad4 ASJ

AF:

0.0576

Gnomad4 EAS

AF:

0.0348

Gnomad4 SAS

AF:

0.0470

Gnomad4 FIN

AF:

0.00349

Gnomad4 NFE

AF:

0.0193

Gnomad4 OTH

AF:

0.0317

Alfa

AF:

0.0231

Hom.:

Bravo

AF:

0.0314

Asia WGS

AF:

0.0320

AC:

111

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 06, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

DANN

Benign

0.54

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over