chr11-119190377-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001145018.3(DRC12):c.556G>A(p.Ala186Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,613,718 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 Uncertain significance (★).
Frequency
Consequence
NM_001145018.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC153 | ENST00000503566.7 | c.556G>A | p.Ala186Thr | missense_variant | Exon 7 of 7 | 5 | NM_001145018.3 | ENSP00000423567.2 | ||
NHERF4 | ENST00000355547.10 | c.*885C>T | downstream_gene_variant | 1 | NM_001168468.2 | ENSP00000347742.5 |
Frequencies
GnomAD3 genomes AF: 0.0000264 AC: 4AN: 151720Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251484Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135918
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461886Hom.: 0 Cov.: 31 AF XY: 0.0000344 AC XY: 25AN XY: 727244
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151832Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74198
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.556G>A (p.A186T) alteration is located in exon 7 (coding exon 6) of the CCDC153 gene. This alteration results from a G to A substitution at nucleotide position 556, causing the alanine (A) at amino acid position 186 to be replaced by a threonine (T). 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