4-2238678-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001303143.2(HAUS3):c.1275G>A(p.Met425Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,461,082 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001303143.2 missense
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 |
---|---|---|---|---|---|---|---|
HAUS3 | NM_001303143.2 | c.1275G>A | p.Met425Ile | missense_variant | 4/6 | ENST00000443786.3 | |
POLN | NM_181808.4 | c.-13+2842G>A | intron_variant | ENST00000511885.6 | |||
HAUS3 | NM_024511.7 | c.1275G>A | p.Met425Ile | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAUS3 | ENST00000443786.3 | c.1275G>A | p.Met425Ile | missense_variant | 4/6 | 1 | NM_001303143.2 | P1 | |
POLN | ENST00000511885.6 | c.-13+2842G>A | intron_variant | 5 | NM_181808.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251036Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135708
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461082Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 726888
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at