chr6-151573472-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_025059.4(CCDC170):c.1073G>A(p.Arg358Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,613,782 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_025059.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC170 | NM_025059.4 | c.1073G>A | p.Arg358Gln | missense_variant | 6/11 | ENST00000239374.8 | |
CCDC170 | XM_011536147.3 | c.1091G>A | p.Arg364Gln | missense_variant | 6/11 | ||
CCDC170 | XM_011536148.3 | c.1091G>A | p.Arg364Gln | missense_variant | 6/10 | ||
CCDC170 | XM_047419372.1 | c.1073G>A | p.Arg358Gln | missense_variant | 6/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC170 | ENST00000239374.8 | c.1073G>A | p.Arg358Gln | missense_variant | 6/11 | 1 | NM_025059.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000564 AC: 14AN: 248438Hom.: 0 AF XY: 0.0000593 AC XY: 8AN XY: 134914
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461502Hom.: 0 Cov.: 34 AF XY: 0.0000165 AC XY: 12AN XY: 727000
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74456
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 07, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at