7-107758925-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_024814.4(CBLL1):c.1223C>T(p.Pro408Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,666 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P408R) has been classified as Uncertain significance.
Frequency
Consequence
NM_024814.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CBLL1 | NM_024814.4 | c.1223C>T | p.Pro408Leu | missense_variant | Exon 6 of 6 | ENST00000440859.8 | NP_079090.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CBLL1 | ENST00000440859.8 | c.1223C>T | p.Pro408Leu | missense_variant | Exon 6 of 6 | 1 | NM_024814.4 | ENSP00000401277.2 | ||
CBLL1 | ENST00000222597.7 | c.1220C>T | p.Pro407Leu | missense_variant | Exon 6 of 6 | 1 | ENSP00000222597.2 | |||
CBLL1 | ENST00000698938.1 | c.1259C>T | p.Pro420Leu | missense_variant | Exon 6 of 6 | ENSP00000514046.1 | ||||
CBLL1 | ENST00000420796.1 | c.*105C>T | downstream_gene_variant | 5 | ENSP00000410615.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152068Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250860Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135580
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461598Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727106
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152068Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74276
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1223C>T (p.P408L) alteration is located in exon 6 (coding exon 6) of the CBLL1 gene. This alteration results from a C to T substitution at nucleotide position 1223, causing the proline (P) at amino acid position 408 to be replaced by a leucine (L). 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