rs12294600
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_145040.3(CAVIN3):c.763C>T(p.Leu255Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0228 in 1,537,122 control chromosomes in the GnomAD database, including 1,416 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_145040.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAVIN3 | NM_145040.3 | c.763C>T | p.Leu255Phe | missense_variant | 2/2 | ENST00000303927.4 | |
LOC101927825 | XR_007062569.1 | n.46G>A | non_coding_transcript_exon_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAVIN3 | ENST00000303927.4 | c.763C>T | p.Leu255Phe | missense_variant | 2/2 | 1 | NM_145040.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0593 AC: 9020AN: 152218Hom.: 694 Cov.: 33
GnomAD3 exomes AF: 0.0255 AC: 4753AN: 186284Hom.: 295 AF XY: 0.0218 AC XY: 2148AN XY: 98446
GnomAD4 exome AF: 0.0188 AC: 25986AN: 1384786Hom.: 721 Cov.: 29 AF XY: 0.0182 AC XY: 12395AN XY: 681818
GnomAD4 genome AF: 0.0594 AC: 9049AN: 152336Hom.: 695 Cov.: 33 AF XY: 0.0576 AC XY: 4291AN XY: 74500
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at