chr18-68838718-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_024781.3(CCDC102B):c.619G>T(p.Val207Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000049 in 1,613,790 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024781.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC102B | NM_024781.3 | c.619G>T | p.Val207Phe | missense_variant | 3/8 | ENST00000360242.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC102B | ENST00000360242.9 | c.619G>T | p.Val207Phe | missense_variant | 3/8 | 1 | NM_024781.3 | P2 | |
CCDC102B | ENST00000584156.5 | c.619G>T | p.Val207Phe | missense_variant | 2/6 | 1 | A2 | ||
CCDC102B | ENST00000584775.5 | c.619G>T | p.Val207Phe | missense_variant | 5/7 | 1 | |||
CCDC102B | ENST00000577772.5 | n.677G>T | non_coding_transcript_exon_variant | 3/7 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000718 AC: 18AN: 250848Hom.: 0 AF XY: 0.0000811 AC XY: 11AN XY: 135596
GnomAD4 exome AF: 0.0000445 AC: 65AN: 1461500Hom.: 0 Cov.: 31 AF XY: 0.0000536 AC XY: 39AN XY: 727056
GnomAD4 genome ? AF: 0.0000919 AC: 14AN: 152290Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 17, 2023 | The c.619G>T (p.V207F) alteration is located in exon 5 (coding exon 2) of the CCDC102B gene. This alteration results from a G to T substitution at nucleotide position 619, causing the valine (V) at amino acid position 207 to be replaced by a phenylalanine (F). 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