15-75640039-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_018285.4(IMP3):c.130G>A(p.Asp44Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000206 in 1,599,174 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018285.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IMP3 | ENST00000403490.3 | c.130G>A | p.Asp44Asn | missense_variant | Exon 1 of 1 | 6 | NM_018285.4 | ENSP00000385217.1 | ||
IMP3 | ENST00000314852.2 | c.130G>A | p.Asp44Asn | missense_variant | Exon 2 of 2 | 2 | ENSP00000326981.2 | |||
ENSG00000275454 | ENST00000621523.1 | n.280C>T | non_coding_transcript_exon_variant | Exon 1 of 1 | 6 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152254Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000138 AC: 3AN: 217492Hom.: 0 AF XY: 0.0000167 AC XY: 2AN XY: 120086
GnomAD4 exome AF: 0.0000200 AC: 29AN: 1446920Hom.: 0 Cov.: 32 AF XY: 0.0000181 AC XY: 13AN XY: 719014
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152254Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.130G>A (p.D44N) alteration is located in exon 1 (coding exon 1) of the IMP3 gene. This alteration results from a G to A substitution at nucleotide position 130, causing the aspartic acid (D) at amino acid position 44 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