rs17362588
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_173648.4(CCDC141):c.2803C>T(p.Arg935Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0762 in 1,608,436 control chromosomes in the GnomAD database, including 5,410 homozygotes. In-silico tool predicts a benign outcome for this variant. 9/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R935Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_173648.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC141 | NM_173648.4 | c.2803C>T | p.Arg935Trp | missense_variant | 18/24 | ENST00000443758.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC141 | ENST00000443758.7 | c.2803C>T | p.Arg935Trp | missense_variant | 18/24 | 5 | NM_173648.4 | P1 | |
ENST00000652826.1 | n.306+27665G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0603 AC: 9155AN: 151946Hom.: 363 Cov.: 32
GnomAD3 exomes AF: 0.0603 AC: 15016AN: 248924Hom.: 570 AF XY: 0.0607 AC XY: 8175AN XY: 134598
GnomAD4 exome AF: 0.0779 AC: 113436AN: 1456372Hom.: 5047 Cov.: 30 AF XY: 0.0768 AC XY: 55638AN XY: 724436
GnomAD4 genome ? AF: 0.0602 AC: 9152AN: 152064Hom.: 363 Cov.: 32 AF XY: 0.0596 AC XY: 4433AN XY: 74336
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | This variant is associated with the following publications: (PMID: 29748316, 30012220) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at