8-22005062-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_015024.5(XPO7):c.3238G>A(p.Val1080Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000136 in 1,612,984 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015024.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
XPO7 | NM_015024.5 | c.3238G>A | p.Val1080Met | missense_variant | Exon 28 of 28 | ENST00000252512.14 | NP_055839.3 | |
XPO7 | NM_001100161.2 | c.3265G>A | p.Val1089Met | missense_variant | Exon 28 of 28 | NP_001093631.1 | ||
XPO7 | NM_001362802.2 | c.3172G>A | p.Val1058Met | missense_variant | Exon 27 of 27 | NP_001349731.1 | ||
XPO7 | NR_156173.2 | n.3458G>A | non_coding_transcript_exon_variant | Exon 29 of 29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
XPO7 | ENST00000252512.14 | c.3238G>A | p.Val1080Met | missense_variant | Exon 28 of 28 | 1 | NM_015024.5 | ENSP00000252512.9 | ||
XPO7 | ENST00000433566.8 | c.3241G>A | p.Val1081Met | missense_variant | Exon 28 of 28 | 5 | ENSP00000410249.3 |
Frequencies
GnomAD3 genomes AF: 0.0000461 AC: 7AN: 151904Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000322 AC: 8AN: 248754Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 134954
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1460964Hom.: 0 Cov.: 33 AF XY: 0.00000688 AC XY: 5AN XY: 726786
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152020Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3238G>A (p.V1080M) alteration is located in exon 28 (coding exon 28) of the XPO7 gene. This alteration results from a G to A substitution at nucleotide position 3238, causing the valine (V) at amino acid position 1080 to be replaced by a methionine (M). 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