chr6-151573432-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_025059.4(CCDC170):c.1033G>A(p.Glu345Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00832 in 1,614,146 control chromosomes in the GnomAD database, including 74 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_025059.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC170 | NM_025059.4 | c.1033G>A | p.Glu345Lys | missense_variant | 6/11 | ENST00000239374.8 | |
CCDC170 | XM_011536147.3 | c.1051G>A | p.Glu351Lys | missense_variant | 6/11 | ||
CCDC170 | XM_011536148.3 | c.1051G>A | p.Glu351Lys | missense_variant | 6/10 | ||
CCDC170 | XM_047419372.1 | c.1033G>A | p.Glu345Lys | missense_variant | 6/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC170 | ENST00000239374.8 | c.1033G>A | p.Glu345Lys | missense_variant | 6/11 | 1 | NM_025059.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00526 AC: 800AN: 152174Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00530 AC: 1320AN: 249272Hom.: 1 AF XY: 0.00525 AC XY: 710AN XY: 135234
GnomAD4 exome AF: 0.00864 AC: 12626AN: 1461854Hom.: 71 Cov.: 35 AF XY: 0.00843 AC XY: 6130AN XY: 727236
GnomAD4 genome ? AF: 0.00526 AC: 801AN: 152292Hom.: 3 Cov.: 32 AF XY: 0.00492 AC XY: 366AN XY: 74460
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | May 05, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | CCDC170: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at