chr1-18883265-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_003748.4(ALDH4A1):c.603+14G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00299 in 1,613,176 control chromosomes in the GnomAD database, including 138 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_003748.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALDH4A1 | NM_003748.4 | c.603+14G>A | intron_variant | Intron 6 of 14 | ENST00000375341.8 | NP_003739.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0161 AC: 2450AN: 152258Hom.: 76 Cov.: 34
GnomAD3 exomes AF: 0.00425 AC: 1061AN: 249888Hom.: 23 AF XY: 0.00299 AC XY: 405AN XY: 135580
GnomAD4 exome AF: 0.00162 AC: 2370AN: 1460800Hom.: 62 Cov.: 33 AF XY: 0.00137 AC XY: 993AN XY: 726732
GnomAD4 genome AF: 0.0161 AC: 2454AN: 152376Hom.: 76 Cov.: 34 AF XY: 0.0155 AC XY: 1152AN XY: 74520
ClinVar
Submissions by phenotype
Hyperprolinemia type 2 Benign:2
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This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at