rs3803426
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000693.4(ALDH1A3):c.*208C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.042 in 571,442 control chromosomes in the GnomAD database, including 904 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.061 ( 480 hom., cov: 33)
Exomes 𝑓: 0.035 ( 424 hom. )
Consequence
ALDH1A3
NM_000693.4 3_prime_UTR
NM_000693.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.465
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=-0.67).
BP6
?
Variant 15-100914981-C-T is Benign according to our data. Variant chr15-100914981-C-T is described in ClinVar as [Benign]. Clinvar id is 1287624.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALDH1A3 | NM_000693.4 | c.*208C>T | 3_prime_UTR_variant | 13/13 | ENST00000329841.10 | ||
ALDH1A3-AS1 | NR_135827.1 | n.480+3823G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALDH1A3 | ENST00000329841.10 | c.*208C>T | 3_prime_UTR_variant | 13/13 | 1 | NM_000693.4 | P1 | ||
ALDH1A3-AS1 | ENST00000656756.1 | n.588+3823G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0614 AC: 9348AN: 152182Hom.: 480 Cov.: 33
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GnomAD4 exome AF: 0.0349 AC: 14647AN: 419142Hom.: 424 Cov.: 4 AF XY: 0.0350 AC XY: 7710AN XY: 219984
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GnomAD4 genome ? AF: 0.0615 AC: 9361AN: 152300Hom.: 480 Cov.: 33 AF XY: 0.0630 AC XY: 4695AN XY: 74476
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 23, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at