rs45612738
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000379.4(XDH):c.1134C>T(p.Gly378=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00389 in 1,613,820 control chromosomes in the GnomAD database, including 194 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000379.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XDH | NM_000379.4 | c.1134C>T | p.Gly378= | splice_region_variant, synonymous_variant | 13/36 | ENST00000379416.4 | |
XDH | XM_011533095.3 | c.1134C>T | p.Gly378= | splice_region_variant, synonymous_variant | 13/36 | ||
XDH | XM_011533096.3 | c.1134C>T | p.Gly378= | splice_region_variant, synonymous_variant | 13/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XDH | ENST00000379416.4 | c.1134C>T | p.Gly378= | splice_region_variant, synonymous_variant | 13/36 | 1 | NM_000379.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0191 AC: 2902AN: 152174Hom.: 84 Cov.: 32
GnomAD3 exomes AF: 0.00522 AC: 1313AN: 251418Hom.: 48 AF XY: 0.00365 AC XY: 496AN XY: 135872
GnomAD4 exome AF: 0.00231 AC: 3371AN: 1461528Hom.: 110 Cov.: 31 AF XY: 0.00199 AC XY: 1445AN XY: 727070
GnomAD4 genome ? AF: 0.0191 AC: 2905AN: 152292Hom.: 84 Cov.: 32 AF XY: 0.0182 AC XY: 1357AN XY: 74474
ClinVar
Submissions by phenotype
Hereditary xanthinuria type 1 Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 06, 2021 | - - |
Xanthinuria type II Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at