chr12-49637555-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001031698.3(PRPF40B):āc.1646T>Cā(p.Val549Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,613,862 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001031698.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRPF40B | NM_001031698.3 | c.1646T>C | p.Val549Ala | missense_variant | 17/26 | ENST00000548825.7 | NP_001026868.2 | |
FMNL3 | NM_175736.5 | c.*8260A>G | 3_prime_UTR_variant | 26/26 | ENST00000335154.10 | NP_783863.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRPF40B | ENST00000548825.7 | c.1646T>C | p.Val549Ala | missense_variant | 17/26 | 5 | NM_001031698.3 | ENSP00000448073 | P3 | |
FMNL3 | ENST00000335154.10 | c.*8260A>G | 3_prime_UTR_variant | 26/26 | 1 | NM_175736.5 | ENSP00000335655 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250948Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135670
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461588Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727088
GnomAD4 genome AF: 0.000171 AC: 26AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.1580T>C (p.V527A) alteration is located in exon 16 (coding exon 16) of the PRPF40B gene. This alteration results from a T to C substitution at nucleotide position 1580, causing the valine (V) at amino acid position 527 to be replaced by an alanine (A). 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