15-100893950-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000693.4(ALDH1A3):c.538-4G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,613,970 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000693.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALDH1A3 | NM_000693.4 | c.538-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000329841.10 | |||
ALDH1A3-AS1 | NR_135827.1 | n.2597C>T | non_coding_transcript_exon_variant | 2/2 | |||
ALDH1A3 | NM_001293815.2 | c.346-1983G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALDH1A3 | ENST00000329841.10 | c.538-4G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000693.4 | P1 | |||
ALDH1A3-AS1 | ENST00000656756.1 | n.2705C>T | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 251008Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135646
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461636Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 727124
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152334Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74486
ClinVar
Submissions by phenotype
Isolated microphthalmia 8 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 30, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at