X-52818208-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001386970.1(XAGE5):c.322C>G(p.Leu108Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000455 in 1,210,100 control chromosomes in the GnomAD database, including 2 homozygotes. There are 10 hemizygotes in GnomAD. 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_001386970.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
XAGE5 | ENST00000375501.2 | c.322C>G | p.Leu108Val | missense_variant | Exon 6 of 6 | 5 | NM_001386970.1 | ENSP00000364651.1 | ||
XAGE5 | ENST00000375503.7 | n.*250C>G | non_coding_transcript_exon_variant | Exon 5 of 5 | 1 | ENSP00000364653.3 | ||||
XAGE5 | ENST00000375503.7 | n.*250C>G | 3_prime_UTR_variant | Exon 5 of 5 | 1 | ENSP00000364653.3 | ||||
XAGE5 | ENST00000445860.2 | n.325C>G | non_coding_transcript_exon_variant | Exon 2 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000276 AC: 31AN: 112516Hom.: 2 Cov.: 23 AF XY: 0.000115 AC XY: 4AN XY: 34664
GnomAD3 exomes AF: 0.0000219 AC: 4AN: 182662Hom.: 0 AF XY: 0.0000446 AC XY: 3AN XY: 67270
GnomAD4 exome AF: 0.0000219 AC: 24AN: 1097584Hom.: 0 Cov.: 29 AF XY: 0.0000165 AC XY: 6AN XY: 363078
GnomAD4 genome AF: 0.000276 AC: 31AN: 112516Hom.: 2 Cov.: 23 AF XY: 0.000115 AC XY: 4AN XY: 34664
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.322C>G (p.L108V) alteration is located in exon 5 (coding exon 4) of the XAGE5 gene. This alteration results from a C to G substitution at nucleotide position 322, causing the leucine (L) at amino acid position 108 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