rs3825926
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000693.4(ALDH1A3):c.1069-287C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0204 in 152,324 control chromosomes in the GnomAD database, including 51 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.020 ( 51 hom., cov: 32)
Consequence
ALDH1A3
NM_000693.4 intron
NM_000693.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.268
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 15-100905236-C-T is Benign according to our data. Variant chr15-100905236-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1189283.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.061 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALDH1A3 | NM_000693.4 | c.1069-287C>T | intron_variant | ENST00000329841.10 | |||
ALDH1A3-AS1 | NR_135827.1 | n.481-9170G>A | intron_variant, non_coding_transcript_variant | ||||
ALDH1A3 | NM_001293815.2 | c.748-287C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALDH1A3 | ENST00000329841.10 | c.1069-287C>T | intron_variant | 1 | NM_000693.4 | P1 | |||
ALDH1A3-AS1 | ENST00000656756.1 | n.589-9170G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0204 AC: 3109AN: 152206Hom.: 51 Cov.: 32
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0204 AC: 3105AN: 152324Hom.: 51 Cov.: 32 AF XY: 0.0228 AC XY: 1696AN XY: 74486
GnomAD4 genome
?
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32
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1696
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74486
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161
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3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at