14-59531887-T-A
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001164399.2(CCDC175):c.1647A>T(p.Gln549His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000129 in 1,236,604 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001164399.2 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC175 | ENST00000537690.7 | c.1647A>T | p.Gln549His | missense_variant | Exon 14 of 20 | 5 | NM_001164399.2 | ENSP00000453940.1 | ||
CCDC175 | ENST00000281581.5 | c.1647A>T | p.Gln549His | missense_variant | Exon 14 of 20 | 5 | ENSP00000452964.1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152234Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000162 AC: 2AN: 123826 AF XY: 0.0000152 show subpopulations
GnomAD4 exome AF: 0.00000646 AC: 7AN: 1084252Hom.: 0 Cov.: 17 AF XY: 0.00000732 AC XY: 4AN XY: 546218 show subpopulations
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152352Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74494 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1647A>T (p.Q549H) alteration is located in exon 14 (coding exon 14) of the CCDC175 gene. This alteration results from a A to T substitution at nucleotide position 1647, causing the glutamine (Q) at amino acid position 549 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at