chr5-83104954-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_003401.5(XRCC4):c.35C>G(p.Ser12Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00141 in 1,613,420 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003401.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XRCC4 | NM_003401.5 | c.35C>G | p.Ser12Cys | missense_variant | 2/8 | ENST00000396027.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XRCC4 | ENST00000396027.9 | c.35C>G | p.Ser12Cys | missense_variant | 2/8 | 5 | NM_003401.5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00717 AC: 1091AN: 152076Hom.: 15 Cov.: 32
GnomAD3 exomes AF: 0.00183 AC: 460AN: 251124Hom.: 5 AF XY: 0.00133 AC XY: 180AN XY: 135758
GnomAD4 exome AF: 0.000810 AC: 1183AN: 1461226Hom.: 18 Cov.: 30 AF XY: 0.000677 AC XY: 492AN XY: 726942
GnomAD4 genome ? AF: 0.00719 AC: 1095AN: 152194Hom.: 16 Cov.: 32 AF XY: 0.00718 AC XY: 534AN XY: 74404
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 23, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at