4-2232061-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001303143.2(HAUS3):āc.1678T>Gā(p.Leu560Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000321 in 1,589,614 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L560S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001303143.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HAUS3 | NM_001303143.2 | c.1678T>G | p.Leu560Val | missense_variant | 6/6 | ENST00000443786.3 | |
POLN | NM_181808.4 | c.-12-2818T>G | intron_variant | ENST00000511885.6 | |||
HAUS3 | NM_024511.7 | c.1678T>G | p.Leu560Val | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAUS3 | ENST00000443786.3 | c.1678T>G | p.Leu560Val | missense_variant | 6/6 | 1 | NM_001303143.2 | P1 | |
POLN | ENST00000511885.6 | c.-12-2818T>G | intron_variant | 5 | NM_181808.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152130Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000163 AC: 4AN: 244926Hom.: 0 AF XY: 0.00000754 AC XY: 1AN XY: 132568
GnomAD4 exome AF: 0.0000306 AC: 44AN: 1437366Hom.: 0 Cov.: 26 AF XY: 0.0000251 AC XY: 18AN XY: 716026
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152248Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74448
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 08, 2023 | The c.1678T>G (p.L560V) alteration is located in exon 5 (coding exon 4) of the HAUS3 gene. This alteration results from a T to G substitution at nucleotide position 1678, causing the leucine (L) at amino acid position 560 to be replaced by a valine (V). 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