chr8-99875441-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_017890.5(VPS13B):c.11844G>C(p.Leu3948=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,864 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L3948L) has been classified as Likely benign.
Frequency
Consequence
NM_017890.5 synonymous
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VPS13B | NM_017890.5 | c.11844G>C | p.Leu3948= | synonymous_variant | 62/62 | ENST00000358544.7 | |
VPS13B | NM_152564.5 | c.11769G>C | p.Leu3923= | synonymous_variant | 62/62 | ENST00000357162.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VPS13B | ENST00000358544.7 | c.11844G>C | p.Leu3948= | synonymous_variant | 62/62 | 1 | NM_017890.5 | ||
VPS13B | ENST00000357162.7 | c.11769G>C | p.Leu3923= | synonymous_variant | 62/62 | 1 | NM_152564.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251020Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135744
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461864Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727240
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Cohen syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 14, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at