7-107749020-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_024814.4(CBLL1):c.154C>T(p.Pro52Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000539 in 1,613,934 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024814.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CBLL1 | NM_024814.4 | c.154C>T | p.Pro52Ser | missense_variant | Exon 2 of 6 | ENST00000440859.8 | NP_079090.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251294Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135826
GnomAD4 exome AF: 0.0000486 AC: 71AN: 1461734Hom.: 0 Cov.: 30 AF XY: 0.0000509 AC XY: 37AN XY: 727156
GnomAD4 genome AF: 0.000105 AC: 16AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.154C>T (p.P52S) alteration is located in exon 2 (coding exon 2) of the CBLL1 gene. This alteration results from a C to T substitution at nucleotide position 154, causing the proline (P) at amino acid position 52 to be replaced by a serine (S). 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