20-32704020-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4BP6_Very_StrongBA1
The NM_053041.3(COMMD7):c.526+3G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00397 in 1,613,748 control chromosomes in the GnomAD database, including 223 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 Benign (★★).
Frequency
Consequence
NM_053041.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COMMD7 | ENST00000278980.11 | c.526+3G>A | splice_region_variant, intron_variant | Intron 8 of 8 | 1 | NM_053041.3 | ENSP00000278980.6 | |||
ENSG00000285382 | ENST00000646357.1 | c.526+3G>A | splice_region_variant, intron_variant | Intron 8 of 8 | ENSP00000493768.1 |
Frequencies
GnomAD3 genomes AF: 0.0216 AC: 3280AN: 152150Hom.: 110 Cov.: 32
GnomAD3 exomes AF: 0.00563 AC: 1401AN: 249056Hom.: 43 AF XY: 0.00423 AC XY: 571AN XY: 135112
GnomAD4 exome AF: 0.00213 AC: 3110AN: 1461480Hom.: 113 Cov.: 33 AF XY: 0.00179 AC XY: 1298AN XY: 727010
GnomAD4 genome AF: 0.0216 AC: 3294AN: 152268Hom.: 110 Cov.: 32 AF XY: 0.0216 AC XY: 1605AN XY: 74462
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at