5-83105065-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_003401.5(XRCC4):c.139+7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000664 in 1,595,242 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_003401.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
XRCC4 | NM_003401.5 | c.139+7C>T | splice_region_variant, intron_variant | Intron 2 of 7 | ENST00000396027.9 | NP_003392.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000256 AC: 39AN: 152064Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000743 AC: 17AN: 228806Hom.: 0 AF XY: 0.0000403 AC XY: 5AN XY: 124104
GnomAD4 exome AF: 0.0000464 AC: 67AN: 1443060Hom.: 0 Cov.: 30 AF XY: 0.0000460 AC XY: 33AN XY: 717550
GnomAD4 genome AF: 0.000256 AC: 39AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.000349 AC XY: 26AN XY: 74406
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 17, 2024 | - - |
Short stature, microcephaly, and endocrine dysfunction Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Sep 28, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at