chr6-32029623-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_StrongBP6_Moderate
The NM_001002029.4(C4B):c.3734C>T(p.Pro1245Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000281 in 149,586 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict 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. P1245P) has been classified as Benign.
Frequency
Consequence
NM_001002029.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C4B | NM_001002029.4 | c.3734C>T | p.Pro1245Leu | missense_variant | 29/41 | ENST00000435363.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C4B | ENST00000435363.7 | c.3734C>T | p.Pro1245Leu | missense_variant | 29/41 | 1 | NM_001002029.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000281 AC: 42AN: 149482Hom.: 0 Cov.: 27
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000748 AC: 109AN: 1457394Hom.: 0 Cov.: 35 AF XY: 0.0000552 AC XY: 40AN XY: 724970
GnomAD4 genome ? AF: 0.000281 AC: 42AN: 149586Hom.: 0 Cov.: 27 AF XY: 0.000302 AC XY: 22AN XY: 72870
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at