17-16708868-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001382000.1(CCDC144A):c.811C>T(p.His271Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,611,784 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001382000.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC144A | NM_001382000.1 | c.811C>T | p.His271Tyr | missense_variant | Exon 5 of 17 | ENST00000399273.5 | NP_001368929.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC144A | ENST00000399273.5 | c.811C>T | p.His271Tyr | missense_variant | Exon 5 of 17 | 1 | NM_001382000.1 | ENSP00000382215.1 | ||
ENSG00000266302 | ENST00000448331.7 | n.811C>T | non_coding_transcript_exon_variant | Exon 5 of 26 | 2 | ENSP00000440655.2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152098Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000723 AC: 18AN: 248858Hom.: 0 AF XY: 0.0000888 AC XY: 12AN XY: 135130
GnomAD4 exome AF: 0.0000295 AC: 43AN: 1459568Hom.: 0 Cov.: 32 AF XY: 0.0000317 AC XY: 23AN XY: 726080
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152216Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74416
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.811C>T (p.H271Y) alteration is located in exon 5 (coding exon 5) of the CCDC144A gene. This alteration results from a C to T substitution at nucleotide position 811, causing the histidine (H) at amino acid position 271 to be replaced by a tyrosine (Y). 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