rs1219935733
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_002940.3(ABCE1):c.403G>A(p.Asp135Asn) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000819 in 1,587,840 control chromosomes in the GnomAD database, with no homozygous occurrence. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002940.3 missense, splice_region
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCE1 | NM_002940.3 | c.403G>A | p.Asp135Asn | missense_variant, splice_region_variant | Exon 5 of 18 | ENST00000296577.9 | NP_002931.2 | |
ABCE1 | NM_001040876.2 | c.403G>A | p.Asp135Asn | missense_variant, splice_region_variant | Exon 5 of 18 | NP_001035809.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000807 AC: 2AN: 247704Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134064
GnomAD4 exome AF: 0.00000766 AC: 11AN: 1435700Hom.: 0 Cov.: 27 AF XY: 0.0000140 AC XY: 10AN XY: 715540
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.403G>A (p.D135N) alteration is located in exon 5 (coding exon 4) of the ABCE1 gene. This alteration results from a G to A substitution at nucleotide position 403, causing the aspartic acid (D) at amino acid position 135 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at