chr5-80320645-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032567.4(SPZ1):āc.430A>Gā(p.Met144Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,613,630 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 Uncertain significance (ā ).
Frequency
Consequence
NM_032567.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPZ1 | NM_032567.4 | c.430A>G | p.Met144Val | missense_variant | 1/1 | ENST00000296739.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPZ1 | ENST00000296739.6 | c.430A>G | p.Met144Val | missense_variant | 1/1 | NM_032567.4 | P1 | ||
SPZ1 | ENST00000511881.1 | c.430A>G | p.Met144Val | missense_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000461 AC: 7AN: 151708Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249372Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135358
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461804Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 727210
GnomAD4 genome AF: 0.0000461 AC: 7AN: 151826Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2AN XY: 74180
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | The c.430A>G (p.M144V) alteration is located in exon 1 (coding exon 1) of the SPZ1 gene. This alteration results from a A to G substitution at nucleotide position 430, causing the methionine (M) at amino acid position 144 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