chrX-143034038-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001009613.4(SPANXN4):āc.92T>Cā(p.Leu31Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000555 in 1,171,662 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 18 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. 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. L31M) has been classified as Uncertain significance.
Frequency
Consequence
NM_001009613.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPANXN4 | NM_001009613.4 | c.92T>C | p.Leu31Pro | missense_variant | 2/2 | ENST00000446864.2 | |
SPANXN4 | XM_017029543.1 | c.92T>C | p.Leu31Pro | missense_variant | 2/4 | ||
SPANXN4 | XM_017029544.1 | c.89T>C | p.Leu30Pro | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPANXN4 | ENST00000446864.2 | c.92T>C | p.Leu31Pro | missense_variant | 2/2 | 1 | NM_001009613.4 | P2 | |
SPANXN4 | ENST00000370504.3 | c.89T>C | p.Leu30Pro | missense_variant | 2/3 | 5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000107 AC: 12AN: 112144Hom.: 0 Cov.: 23 AF XY: 0.0000874 AC XY: 3AN XY: 34316
GnomAD3 exomes AF: 0.0000326 AC: 4AN: 122660Hom.: 0 AF XY: 0.0000259 AC XY: 1AN XY: 38560
GnomAD4 exome AF: 0.0000500 AC: 53AN: 1059518Hom.: 0 Cov.: 31 AF XY: 0.0000435 AC XY: 15AN XY: 344768
GnomAD4 genome AF: 0.000107 AC: 12AN: 112144Hom.: 0 Cov.: 23 AF XY: 0.0000874 AC XY: 3AN XY: 34316
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2024 | The c.92T>C (p.L31P) alteration is located in exon 2 (coding exon 2) of the SPANXN4 gene. This alteration results from a T to C substitution at nucleotide position 92, causing the leucine (L) at amino acid position 31 to be replaced by a proline (P). 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