16-74887695-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_030581.4(WDR59):c.2407G>T(p.Gly803Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00225 in 1,614,082 control chromosomes in the GnomAD database, including 84 homozygotes. 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 Benign (★★).
Frequency
Consequence
NM_030581.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0124 AC: 1881AN: 152154Hom.: 42 Cov.: 32
GnomAD3 exomes AF: 0.00315 AC: 790AN: 251102Hom.: 15 AF XY: 0.00231 AC XY: 313AN XY: 135748
GnomAD4 exome AF: 0.00120 AC: 1751AN: 1461810Hom.: 42 Cov.: 30 AF XY: 0.00101 AC XY: 731AN XY: 727220
GnomAD4 genome AF: 0.0124 AC: 1881AN: 152272Hom.: 42 Cov.: 32 AF XY: 0.0117 AC XY: 875AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at