19-41316773-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_052848.3(CCDC97):c.436C>T(p.Arg146Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000127 in 1,609,012 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_052848.3 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 |
---|---|---|---|---|---|---|---|---|---|---|
CCDC97 | ENST00000269967.4 | c.436C>T | p.Arg146Trp | missense_variant | Exon 2 of 5 | 1 | NM_052848.3 | ENSP00000269967.2 | ||
TGFB1 | ENST00000598758.5 | n.303-14053G>A | intron_variant | Intron 2 of 3 | 5 | |||||
CCDC97 | ENST00000596882.1 | c.*192C>T | downstream_gene_variant | 3 | ENSP00000470858.1 |
Frequencies
GnomAD3 genomes AF: 0.000552 AC: 84AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000153 AC: 37AN: 242166Hom.: 0 AF XY: 0.000159 AC XY: 21AN XY: 131848
GnomAD4 exome AF: 0.0000831 AC: 121AN: 1456674Hom.: 0 Cov.: 33 AF XY: 0.0000843 AC XY: 61AN XY: 723636
GnomAD4 genome AF: 0.000551 AC: 84AN: 152338Hom.: 0 Cov.: 32 AF XY: 0.000497 AC XY: 37AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.436C>T (p.R146W) alteration is located in exon 2 (coding exon 2) of the CCDC97 gene. This alteration results from a C to T substitution at nucleotide position 436, causing the arginine (R) at amino acid position 146 to be replaced by a tryptophan (W). 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