15-75639940-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_018285.4(IMP3):c.229G>A(p.Ala77Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000412 in 1,454,764 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. 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 -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IMP3 | ENST00000403490.3 | c.229G>A | p.Ala77Thr | missense_variant | Exon 1 of 1 | 6 | NM_018285.4 | ENSP00000385217.1 | ||
IMP3 | ENST00000314852.2 | c.229G>A | p.Ala77Thr | missense_variant | Exon 2 of 2 | 2 | ENSP00000326981.2 | |||
ENSG00000275454 | ENST00000621523.1 | n.181C>T | non_coding_transcript_exon_variant | Exon 1 of 1 | 6 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 exomes AF: 0.00000440 AC: 1AN: 227500Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 125474
GnomAD4 exome AF: 0.00000412 AC: 6AN: 1454764Hom.: 0 Cov.: 32 AF XY: 0.00000553 AC XY: 4AN XY: 723352
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.229G>A (p.A77T) 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 229, causing the alanine (A) at amino acid position 77 to be replaced by a threonine (T). 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