7-142943509-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_000420.3(KEL):āc.1680A>Cā(p.Pro560Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0551 in 1,613,774 control chromosomes in the GnomAD database, including 3,365 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_000420.3 synonymous
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KEL | NM_000420.3 | c.1680A>C | p.Pro560Pro | synonymous_variant | Exon 15 of 19 | ENST00000355265.7 | NP_000411.1 | |
KEL | XM_005249993.2 | c.1716A>C | p.Pro572Pro | synonymous_variant | Exon 15 of 19 | XP_005250050.1 | ||
KEL | XM_047420357.1 | c.1569A>C | p.Pro523Pro | synonymous_variant | Exon 14 of 18 | XP_047276313.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KEL | ENST00000355265.7 | c.1680A>C | p.Pro560Pro | synonymous_variant | Exon 15 of 19 | 1 | NM_000420.3 | ENSP00000347409.2 | ||
KEL | ENST00000470850.1 | n.145A>C | non_coding_transcript_exon_variant | Exon 2 of 4 | 2 | |||||
KEL | ENST00000465697.1 | n.*40A>C | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0880 AC: 13387AN: 152070Hom.: 877 Cov.: 33
GnomAD3 exomes AF: 0.0505 AC: 12687AN: 251368Hom.: 529 AF XY: 0.0464 AC XY: 6301AN XY: 135830
GnomAD4 exome AF: 0.0517 AC: 75536AN: 1461586Hom.: 2485 Cov.: 33 AF XY: 0.0496 AC XY: 36093AN XY: 727110
GnomAD4 genome AF: 0.0881 AC: 13407AN: 152188Hom.: 880 Cov.: 33 AF XY: 0.0862 AC XY: 6412AN XY: 74406
ClinVar
Submissions by phenotype
KEL-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at