Variant 15-100879560-T-A 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 XM_047433433.1(LOC124903575):c.244A>T(p.Ser82Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 147,756 control chromosomes in the GnomAD database, including 2,436 homozygotes. In-silico tool predicts a benign outcome for this variant. 5/5 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 2436 hom., cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

LOC124903575
XM_047433433.1 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.14

Variant links:

Genes affected

LOC124903575 (HGNC:):

LOC124903575 links:

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=-0.87).

BP6

Variant 15-100879560-T-A is Benign according to our data. Variant chr15-100879560-T-A is described in ClinVar as [Benign]. Clinvar id is 1286413.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903575	XM_047433433.1 link	c.244A>T	p.Ser82Cys	missense_variant	1/1		XP_047289389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALDH1A3	ENST00000561338.5 link	c.15+1695T>A		intron_variant		4		ENSP00000452789.1		H0YKF9
ENSG00000272639	ENST00000558568.1 link	n.502-5707T>A		intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15300

AN:

147648

Hom.:

2426

Cov.:

show subpopulations

Gnomad AFR

AF:

0.343

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0375

Gnomad ASJ

AF:

0.00118

Gnomad EAS

AF:

0.0211

Gnomad SAS

AF:

0.00748

Gnomad FIN

AF:

0.0230

Gnomad MID

AF:

0.0159

Gnomad NFE

AF:

0.00303

Gnomad OTH

AF:

0.0723

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

108

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

Gnomad4 AMR exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.104

AC:

15360

AN:

147756

Hom.:

2436

Cov.:

AF XY:

0.102

AC XY:

7319

AN XY:

71950

show subpopulations

Gnomad4 AFR

AF:

0.343

Gnomad4 AMR

AF:

0.0374

Gnomad4 ASJ

AF:

0.00118

Gnomad4 EAS

AF:

0.0212

Gnomad4 SAS

AF:

0.00748

Gnomad4 FIN

AF:

0.0230

Gnomad4 NFE

AF:

0.00303

Gnomad4 OTH

AF:

0.0759

Alfa

AF:

0.0511

Hom.:

150

Asia WGS

AF:

0.0550

AC:

157

AN:

2892

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	clinical testing	GeneDx	Aug 03, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.0

DANN

Benign

0.59

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