NM_003401.5:c.921T>G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_003401.5(XRCC4):c.921T>G(p.Ser307Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 1,609,882 control chromosomes in the GnomAD database, including 34,606 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. S307S) has been classified as Likely benign.
Frequency
Consequence
NM_003401.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
XRCC4 | NM_003401.5 | c.921T>G | p.Ser307Ser | synonymous_variant | Exon 8 of 8 | ENST00000396027.9 | NP_003392.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
XRCC4 | ENST00000396027.9 | c.921T>G | p.Ser307Ser | synonymous_variant | Exon 8 of 8 | 5 | NM_003401.5 | ENSP00000379344.4 | ||
XRCC4 | ENST00000511817.1 | c.927T>G | p.Ser309Ser | synonymous_variant | Exon 8 of 8 | 1 | ENSP00000421491.1 | |||
XRCC4 | ENST00000282268.7 | c.921T>G | p.Ser307Ser | synonymous_variant | Exon 8 of 8 | 1 | ENSP00000282268.3 | |||
XRCC4 | ENST00000338635.10 | c.927T>G | p.Ser309Ser | synonymous_variant | Exon 8 of 8 | 2 | ENSP00000342011.6 |
Frequencies
GnomAD3 genomes AF: 0.254 AC: 38568AN: 151890Hom.: 7025 Cov.: 32
GnomAD3 exomes AF: 0.233 AC: 57829AN: 247880Hom.: 11025 AF XY: 0.214 AC XY: 28746AN XY: 134114
GnomAD4 exome AF: 0.152 AC: 221782AN: 1457874Hom.: 27552 Cov.: 31 AF XY: 0.150 AC XY: 108881AN XY: 725260
GnomAD4 genome AF: 0.254 AC: 38640AN: 152008Hom.: 7054 Cov.: 32 AF XY: 0.260 AC XY: 19284AN XY: 74310
ClinVar
Submissions by phenotype
not provided Benign:2
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Short stature, microcephaly, and endocrine dysfunction Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at