chr14-22951628-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001166269.2(HAUS4):c.392G>A(p.Ser131Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000991 in 1,613,848 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001166269.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HAUS4 | NM_001166269.2 | c.392G>A | p.Ser131Asn | missense_variant | Exon 5 of 10 | ENST00000541587.6 | NP_001159741.1 | |
HAUS4 | NM_017815.3 | c.392G>A | p.Ser131Asn | missense_variant | Exon 5 of 10 | NP_060285.2 | ||
HAUS4 | NM_001166270.2 | c.330+700G>A | intron_variant | Intron 4 of 8 | NP_001159742.1 | |||
PRMT5-DT | NR_110002.1 | n.195-2703C>T | intron_variant | Intron 2 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HAUS4 | ENST00000541587.6 | c.392G>A | p.Ser131Asn | missense_variant | Exon 5 of 10 | 1 | NM_001166269.2 | ENSP00000441026.1 | ||
ENSG00000259132 | ENST00000555074.1 | c.50-3615G>A | intron_variant | Intron 1 of 4 | 2 | ENSP00000450856.2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152116Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251448Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135902
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461732Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727168
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152116Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.392G>A (p.S131N) alteration is located in exon 5 (coding exon 4) of the HAUS4 gene. This alteration results from a G to A substitution at nucleotide position 392, causing the serine (S) at amino acid position 131 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