19-6465557-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_139161.5(CRB3):c.95C>T(p.Ser32Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,613,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_139161.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CRB3 | NM_139161.5 | c.95C>T | p.Ser32Phe | missense_variant | Exon 3 of 4 | ENST00000600229.6 | NP_631900.1 | |
CRB3 | NM_174881.4 | c.95C>T | p.Ser32Phe | missense_variant | Exon 3 of 5 | NP_777377.1 | ||
CRB3 | NM_174882.3 | c.95C>T | p.Ser32Phe | missense_variant | Exon 3 of 4 | NP_777378.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRB3 | ENST00000600229.6 | c.95C>T | p.Ser32Phe | missense_variant | Exon 3 of 4 | 2 | NM_139161.5 | ENSP00000472010.1 | ||
CRB3 | ENST00000356762.7 | c.95C>T | p.Ser32Phe | missense_variant | Exon 3 of 5 | 1 | ENSP00000349204.2 | |||
CRB3 | ENST00000308243.7 | c.95C>T | p.Ser32Phe | missense_variant | Exon 2 of 3 | 2 | ENSP00000310123.6 | |||
CRB3 | ENST00000598494.5 | c.95C>T | p.Ser32Phe | missense_variant | Exon 3 of 4 | 2 | ENSP00000469707.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251468Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135908
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461694Hom.: 0 Cov.: 30 AF XY: 0.00000963 AC XY: 7AN XY: 727168
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.95C>T (p.S32F) alteration is located in exon 3 (coding exon 2) of the CRB3 gene. This alteration results from a C to T substitution at nucleotide position 95, causing the serine (S) at amino acid position 32 to be replaced by a phenylalanine (F). 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