chr5-157285430-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001037333.3(CYFIP2):c.69C>T(p.Pro23=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,582,064 control chromosomes in the GnomAD database, including 1 homozygotes. 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. P23P) has been classified as Likely benign.
Frequency
Consequence
NM_001037333.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYFIP2 | NM_001037333.3 | c.69C>T | p.Pro23= | synonymous_variant | 2/31 | ENST00000620254.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYFIP2 | ENST00000620254.5 | c.69C>T | p.Pro23= | synonymous_variant | 2/31 | 1 | NM_001037333.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000496 AC: 10AN: 201468Hom.: 1 AF XY: 0.0000558 AC XY: 6AN XY: 107588
GnomAD4 exome AF: 0.0000252 AC: 36AN: 1429790Hom.: 1 Cov.: 31 AF XY: 0.0000254 AC XY: 18AN XY: 707852
GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74450
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 25, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at