chrX-143034239-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001009613.4(SPANXN4):āc.293A>Gā(p.Gln98Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000146 in 1,163,612 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 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 ).
Frequency
Consequence
NM_001009613.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPANXN4 | NM_001009613.4 | c.293A>G | p.Gln98Arg | missense_variant | 2/2 | ENST00000446864.2 | |
SPANXN4 | XM_017029543.1 | c.286+7A>G | splice_region_variant, intron_variant | ||||
SPANXN4 | XM_017029544.1 | c.283+7A>G | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPANXN4 | ENST00000446864.2 | c.293A>G | p.Gln98Arg | missense_variant | 2/2 | 1 | NM_001009613.4 | P2 | |
SPANXN4 | ENST00000370504.3 | c.283+7A>G | splice_region_variant, intron_variant | 5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00000890 AC: 1AN: 112356Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34500
GnomAD3 exomes AF: 0.0000606 AC: 7AN: 115464Hom.: 0 AF XY: 0.000112 AC XY: 4AN XY: 35804
GnomAD4 exome AF: 0.0000152 AC: 16AN: 1051204Hom.: 0 Cov.: 30 AF XY: 0.0000206 AC XY: 7AN XY: 339196
GnomAD4 genome AF: 0.00000890 AC: 1AN: 112408Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34562
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2023 | The c.293A>G (p.Q98R) alteration is located in exon 2 (coding exon 2) of the SPANXN4 gene. This alteration results from a A to G substitution at nucleotide position 293, causing the glutamine (Q) at amino acid position 98 to be replaced by an arginine (R). 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